Journal name: Journal of Proteome Research / Subject term: liquid chromatography

1. Acid/Salt/pH Gradient Improved Resolution and Sensitivity in Proteomics Study Using 2D SCX-RP LC–MS

Author:: Zhu Ming-Zhi; Li Na; Wang Yi-Tong; Liu Ning; Guo Ming-Quan; Sun Bao-qing; Zhou Hua; Liu Liang; Wu Jian-Lin
Source:: Journal of Proteome Research 2017 v.16 no.9 pp. 3470-3475
ISSN:: 1535-3907
Subject:: cation exchange; fractionation; hydrophilicity; hydrophobic bonding; liquid chromatography; mass spectrometry; pH; peptides; proteins; proteome; proteomics
Abstract:: ... The usage of strong cation exchange (SCX) chromatography in proteomics is limited by its poor resolution and nonspecific hydrophobic interactions with peptides, which lead to peptide overlap across fractions and change of peptide retention, respectively. The application of high concentration of salt (up to 1000 mM) in SCX also restricted its use in online 2D SCX-RP LC. In the present research, we ...
DOI:: 10.1021/acs.jproteome.7b00443
: https://doi.org/10.1021/acs.jproteome.7b00443

2. An IonStar Experimental Strategy for MS1 Ion Current-Based Quantification Using Ultrahigh-Field Orbitrap: Reproducible, In-Depth, and Accurate Protein Measurement in Large Cohorts

Author:: Shen Xiaomeng; Shen Shichen; Li Jun; Hu Qiang; Nie Lei; Tu Chengjian; Wang Xue; Orsburn Benjamin; Wang Jianmin; Qu Jun
Source:: Journal of Proteome Research 2017 v.16 no.7 pp. 2445-2456
ISSN:: 1535-3907
Subject:: biomarkers; fractionation; hydrophilicity; hydrophobicity; liquid chromatography; mass spectrometry; monitoring; peptides; proteins; proteome; proteomics
Abstract:: ... In-depth and reproducible protein measurement in many biological samples is often critical for pharmaceutical/biomedical proteomics but remains challenging. MS1-based quantification using quadrupole/ultrahigh-field Orbitrap (Q/UHF-Orbitrap) holds great promise, but the critically important experimental approaches enabling reliable large-cohort analysis have long been overlooked. Here we described ...
DOI:: 10.1021/acs.jproteome.7b00061
PubMed:: 28412812
PubMed Central:: PMC5914162
: https://doi.org/10.1021/acs.jproteome.7b00061

3. Brachyspira hyodysenteriae Infection Regulates Mucin Glycosylation Synthesis Inducing an Increased Expression of Core-2 O-Glycans in Porcine Colon

Author:: Venkatakrishnan Vignesh; Quintana-Hayashi Macarena P.; Mahu Maxime; Haesebrouck Freddy; Pasmans Frank; Lindén Sara K.
Source:: Journal of Proteome Research 2017 v.16 no.4 pp. 1728-1742
ISSN:: 1535-3907
Subject:: Brachyspira hyodysenteriae; binding sites; carbon; colon; epitopes; glycosylation; host-pathogen relationships; industry; liquid chromatography; mucins; mucus; pathogens; polysaccharides; proteome; secretion; swine; swine dysentery; tandem mass spectrometry; tissues; transferases
Abstract:: ... Brachyspira hyodysenteriae causes swine dysentery (SD), leading to global financial losses to the pig industry. Infection with this pathogen results in an increase in B. hyodysenteriae binding sites on mucins, along with increased colonic mucin secretion. We predict that B. hyodysenteriae modifies the glycosylation pattern of the porcine intestinal mucus layer to optimize its host niche. We charac ...
DOI:: 10.1021/acs.jproteome.7b00002
: https://doi.org/10.1021/acs.jproteome.7b00002

4. Discrimination of Four Marine Biofilm-Forming Bacteria by LC–MS Metabolomics and Influence of Culture Parameters

Author:: Favre Laurie; Ortalo-Magné Annick; Greff Stéphane; Pérez Thierry; Thomas Olivier P.; Martin Jean-Charles; Culioli Gérald
Source:: Journal of Proteome Research 2017 v.16 no.5 pp. 1962-1975
ISSN:: 1535-3907
Subject:: Pseudoalteromonas; Shewanella; amides; aquatic bacteria; biofilm; biomarkers; culture media; developmental stages; hydroxylation; least squares; lipids; liquid chromatography; mass spectrometry; metabolism; metabolites; metabolome; metabolomics; models; ornithine; plankton; proteome; putrescine
Abstract:: ... Most marine bacteria can form biofilms, and they are the main components of biofilms observed on marine surfaces. Biofilms constitute a widespread life strategy, as growing in such structures offers many important biological benefits. The molecular compounds expressed in biofilms and, more generally, the metabolomes of marine bacteria remain poorly studied. In this context, a nontargeted LC–MS met ...
DOI:: 10.1021/acs.jproteome.6b01027
: https://doi.org/10.1021/acs.jproteome.6b01027

5. Effect of Antibiotics and Diet on Enterolactone Concentration and Metabolome Studied by Targeted and Nontargeted LC–MS Metabolomics

Author:: Bolvig Anne K.; Nørskov Natalja P.; Hedemann Mette S.; Foldager Leslie; McCarthy-Sinclair Brendan; Marco Maria L.; Lærke Helle N.; Bach Knudsen Knud E.
Source:: Journal of Proteome Research 2017 v.16 no.6 pp. 2135-2150
ISSN:: 1535-3907
Subject:: antibiotics; blood lipids; diet; epidemiological studies; humans; intestinal microorganisms; lignans; lipid composition; liquid chromatography; low density lipoprotein cholesterol; mass spectrometry; metabolism; metabolites; metabolome; metabolomics; microbial communities; proteome; ribosomal RNA; sequence analysis; swine; swine feeding
Abstract:: ... High plant lignan intake is associated with a number of health benefits, possibly induced by the lignan metabolite enterolactone (ENL). The gut microbiota plays a crucial role in converting dietary lignans into ENL, and epidemiological studies have shown that use of antibiotics is associated with lower levels of ENL. Here we investigate the link between antibiotic use and lignan metabolism in pigs ...
DOI:: 10.1021/acs.jproteome.6b00942
: https://doi.org/10.1021/acs.jproteome.6b00942

6. Elucidating Escherichia coli Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database

Author:: Dai Yunxiang; Shortreed Michael R.; Scalf Mark; Frey Brian L.; Cesnik Anthony J.; Solntsev Stefan; Schaffer Leah V.; Smith Lloyd M.
Source:: Journal of Proteome Research 2017 v.16 no.11 pp. 4156-4165
ISSN:: 1535-3907
Subject:: Escherichia coli; amino acid sequences; databases; genes; isotope labeling; liquid chromatography; lysine; mass spectrometry; models; post-translational modification; proteins; proteome; proteomics
Abstract:: ... A proteoform family is a group of related molecular forms of a protein (proteoforms) derived from the same gene. We have previously described a strategy to identify proteoforms and elucidate proteoform families in complex mixtures of intact proteins. The strategy is based upon measurements of two properties for each proteoform: (i) the accurate proteoform intact-mass, measured by liquid chromatogr ...
DOI:: 10.1021/acs.jproteome.7b00516
PubMed:: 28968100
PubMed Central:: PMC5679780
: https://doi.org/10.1021/acs.jproteome.7b00516

7. Feasibility of Early Detection of Cystic Fibrosis Acute Pulmonary Exacerbations by Exhaled Breath Condensate Metabolomics: A Pilot Study

Author:: Zang Xiaoling; Monge María Eugenia; McCarty Nael A.; Stecenko Arlene A.; Fernández Facundo M.
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 550-558
ISSN:: 1535-3907
Subject:: condensates; cystic fibrosis; death; lactic acid; liquid chromatography; lung function; metabolites; metabolomics; models; monitoring; patients; prediction; proteome
Abstract:: ... Progressive lung function decline and, ultimately, respiratory failure are the most common cause of death in patients with cystic fibrosis (CF). This decline is punctuated by acute pulmonary exacerbations (APEs), and in many cases, there is a failure to return to baseline lung function. Ultraperformance liquid chromatography quadrupole-time-of-flight mass spectrometry was used to profile metabolit ...
DOI:: 10.1021/acs.jproteome.6b00675
: https://doi.org/10.1021/acs.jproteome.6b00675

8. Flagging False Positives Following Untargeted LC–MS Characterization of Histone Post-Translational Modification Combinations

Author:: Willems Sander; Dhaenens Maarten; Govaert Elisabeth; De Clerck Laura; Meert Paulien; Van Neste Christophe; Van Nieuwerburgh Filip; Deforce Dieter
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 655-664
ISSN:: 1535-3907
Subject:: data collection; databases; epigenetics; histones; liquid chromatography; mass spectrometry; models; post-translational modification; proteome; quality control
Abstract:: ... Epigenetic changes can be studied with an untargeted characterization of histone post-translational modifications (PTMs) by liquid chromatography–mass spectrometry (LC–MS). While prior information about more than 20 types of histone PTMs exists, little is known about histone PTM combinations (PTMCs). Because of the combinatorial explosion it is intrinsically impossible to consider all potential PT ...
DOI:: 10.1021/acs.jproteome.6b00724
: https://doi.org/10.1021/acs.jproteome.6b00724

9. Identification of Alternative Splice Variants Using Unique Tryptic Peptide Sequences for Database Searches

Author:: Tran Trung T.; Bollineni Ravi C.; Strozynski Margarita; Koehler Christian J.; Thiede Bernd
Source:: Journal of Proteome Research 2017 v.16 no.7 pp. 2571-2578
ISSN:: 1535-3907
Subject:: T-lymphocytes; alternative splicing; apoptosis; cell lines; databases; eukaryotic cells; genes; humans; liquid chromatography; mass spectrometry; messenger RNA; peptides; proteome; proteomics
Abstract:: ... Alternative splicing is a mechanism in eukaryotes by which different forms of mRNAs are generated from the same gene. Identification of alternative splice variants requires the identification of peptides specific for alternative splice forms. For this purpose, we generated a human database that contains only unique tryptic peptides specific for alternative splice forms from Swiss-Prot entries. Usi ...
DOI:: 10.1021/acs.jproteome.7b00126
: https://doi.org/10.1021/acs.jproteome.7b00126

10. Improved Reversed Phase Chromatography of Hydrophilic Peptides from Spatial and Temporal Changes in Column Temperature

Author:: Young Clifford; Podtelejnikov Alexandre V.; Nielsen Michael L.
Source:: Journal of Proteome Research 2017 v.16 no.6 pp. 2307-2317
ISSN:: 1535-3907
Subject:: bovine serum albumin; electrospray ionization mass spectrometry; equipment; hydrophilicity; peptides; post-translational modification; proteome; proteomics; reversed-phase liquid chromatography; temperature; temporal variation
Abstract:: ... Reversed phase chromatography is an established method for peptide separation and frequently coupled to electrospray ionization–mass spectrometry for proteomic analysis. Column temperature is one parameter that influences peptide retention and elution, but it is often overlooked as its implementation requires additional equipment and method optimization. An apparatus that allows temperature manipu ...
DOI:: 10.1021/acs.jproteome.6b01055
: https://doi.org/10.1021/acs.jproteome.6b01055

11. Mass Spectrometric Analysis of SOX11-Binding Proteins in Head and Neck Cancer Cells Demonstrates the Interaction of SOX11 and HSP90α

Author:: Elzakra Naseim; Cui Li; Liu Tong; Li Hong; Huang Junwei; Hu Shen
Source:: Journal of Proteome Research 2017 v.16 no.11 pp. 3961-3968
ISSN:: 1535-3907
Subject:: Western blotting; cell adhesion; cell lines; gene expression; gene ontology; genes; head and neck neoplasms; humans; keratinocytes; liquid chromatography; neoplasm cells; patients; precipitin tests; protein synthesis; proteins; proteome; survival rate; tandem mass spectrometry; tissues
Abstract:: ... Deregulated expression of SOX11 has been shown to be involved in the progression of various types of cancer. However, the role of SOX11 in head and neck cancer remains largely unknown. In this study, coimmunoprecipitation (Co-IP) and liquid chromatography–tandem mass spectrometry (LC–MS/MS) were performed to identify the proteins that bind to SOX11 at significantly higher levels in head and neck c ...
DOI:: 10.1021/acs.jproteome.7b00247
: https://doi.org/10.1021/acs.jproteome.7b00247

12. Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues

Author:: Zhou Jian-Ying; Chen Lijun; Zhang Bai; Tian Yuan; Liu Tao; Thomas Stefani N.; Chen Li; Schnaubelt Michael; Boja Emily; Hiltke Tara; Kinsinger Christopher R.; Rodriguez Henry; Davies Sherri R.; Li Shunqiang; Snider Jacqueline E.; Erdmann-Gilmore Petra; Tabb David L.; Townsend R. Reid; Ellis Matthew J.; Rodland Karin D.; Smith Richard D.; Carr Steven A.; Zhang Zhen; Chan Daniel W.; Zhang Hui
Source:: Journal of Proteome Research 2017 v.16 no.12 pp. 4523-4530
ISSN:: 1535-3907
Subject:: breast neoplasms; data collection; experimental design; humans; liquid chromatography; mass spectrometry; proteome; proteomics; statistical analysis; tissues
Abstract:: ... Clinical proteomics requires large-scale analysis of human specimens to achieve statistical significance. We evaluated the long-term reproducibility of an iTRAQ (isobaric tags for relative and absolute quantification)-based quantitative proteomics strategy using one channel for reference across all samples in different iTRAQ sets. A total of 148 liquid chromatography tandem mass spectrometric (LC– ...
DOI:: 10.1021/acs.jproteome.7b00362
PubMed:: 29124938
PubMed Central:: PMC5850958
: https://doi.org/10.1021/acs.jproteome.7b00362

13. Quantitation of 87 Proteins by nLC-MRM/MS in Human Plasma: Workflow for Large-Scale Analysis of Biobank Samples

Author:: Rezeli Melinda; Sjödin Karin; Lindberg Henrik; Gidlöf Olof; Lindahl Bertil; Jernberg Tomas; Spaak Jonas; Erlinge David; Marko-Varga György
Source:: Journal of Proteome Research 2017 v.16 no.9 pp. 3242-3254
ISSN:: 1535-3907
Subject:: apolipoprotein E; blood proteins; chemistry; humans; isotope dilution technique; liquid chromatography; monitoring; myocardial infarction; patients; proteome; screening; stable isotopes
Abstract:: ... A multiple reaction monitoring (MRM) assay was developed for precise quantitation of 87 plasma proteins including the three isoforms of apolipoprotein E (APOE) associated with cardiovascular diseases using nanoscale liquid chromatography separation and stable isotope dilution strategy. The analytical performance of the assay was evaluated and we found an average technical variation of 4.7% in 4–5 ...
DOI:: 10.1021/acs.jproteome.7b00235
: https://doi.org/10.1021/acs.jproteome.7b00235

14. Therapeutic Mechanistic Studies of ShuFengJieDu Capsule in an Acute Lung Injury Animal Model Using Quantitative Proteomics Technology

Author:: Tao Zhengang; Meng Xia; Han Yan-qi; Xue Ming-ming; Wu Shifei; Wu Ping; Yuan Ying; Zhu Qiang; Zhang Tie-Jun; Wong Catherine C. L.
Source:: Journal of Proteome Research 2017 v.16 no.11 pp. 4009-4019
ISSN:: 1535-3907
Subject:: Food and Drug Administration; Oriental traditional medicine; animal models; apoptosis; gene ontology; guidelines; immunomodulation; inflammation; lipopolysaccharides; liquid chromatography; loss-of-function mutation; lungs; macrophages; mass spectrometry; medicinal plants; oxidative stress; proteins; proteome; proteomics; rats; respiratory tract diseases; China
Abstract:: ... ShuFengJieDu capsule (SFJDC), a traditional Chinese medicine (TCM) that contains eight medicinal herbs, has been extensively utilized for the treatment of acute lung injury (ALI) and respiratory infections for more than 30 years in China. SFJDC has also been listed in the official guidelines of the China Food and Drug Administration (CFDA) due to its stable clinical manifestations. However, the un ...
DOI:: 10.1021/acs.jproteome.7b00409
: https://doi.org/10.1021/acs.jproteome.7b00409

15. Urine Metabonomics Reveals Early Biomarkers in Diabetic Cognitive Dysfunction

Author:: Song Lili; Zhuang Pengwei; Lin Mengya; Kang Mingqin; Liu Hongyue; Zhang Yuping; Yang Zhen; Chen Yunlong; Zhang Yanjun
Source:: Journal of Proteome Research 2017 v.16 no.9 pp. 3180-3189
ISSN:: 1535-3907
Subject:: animal disease models; biomarkers; cognition; dementia; diabetic complications; early diagnosis; encephalopathy; glutathione; liquid chromatography; mass spectrometry; metabolism; metabolites; metabolomics; mice; nicotinamide; prediction; proteome; sphingolipids; support vector machines; tryptophan; urine
Abstract:: ... Recently, increasing attention has been paid to diabetic encephalopathy, which is a frequent diabetic complication and affects nearly 30% of diabetics. Because cognitive dysfunction from diabetic encephalopathy might develop into irreversible dementia, early diagnosis and detection of this disease is of great significance for its prevention and treatment. This study is to investigate the early spe ...
DOI:: 10.1021/acs.jproteome.7b00168
: https://doi.org/10.1021/acs.jproteome.7b00168

16. Virulent and Vaccine Strains of Streptococcus equi ssp. zooepidemicus Have Different Influences on Phagocytosis and Cytokine Secretion of Macrophages

Author:: Jie Peng; Zhe Ma; Chengwei Hua; Huixing Lin; Hui Zhang; Chengping Lu; Hongjie Fan
Source:: Journal of Proteome Research 2017 v.16 no.1 pp. 77-86
ISSN:: 1535-3907
Subject:: Western blotting; amino acids; bioinformatics; cell culture; cytokines; cytoskeleton; gene ontology; genes; immune response; industry; isotope labeling; liquid chromatography; live vaccines; macrophages; mass spectrometry; pathogens; phagocytosis; phenotype; proteins; proteome; proteomics; quantitative polymerase chain reaction; secretion; stable isotopes; swine; therapeutics; transcription (genetics); vaccine development; virulence; virulent strains
Abstract:: ... Swine streptococcosis is a significant threat to the Chinese pig industry, and Streptococcus equi ssp. zooepidemicus (SEZ) is one of the major pathogens. SEZ ATCC35246 is a classical virulent strain, while SEZ ST171 is a Chinese attenuated vaccine strain. In this study, we employed stable isotope labeling by amino acids in cell culture and liquid chromatography–mass spectrometry (LC–MS) to determi ...
DOI:: 10.1021/acs.jproteome.6b00571
: https://doi.org/10.1021/acs.jproteome.6b00571

17. A Surface Biotinylation Strategy for Reproducible Plasma Membrane Protein Purification and Tracking of Genetic and Drug-Induced Alterations

Author:: Hörmann Katrin; Stukalov Alexey; Müller André C.; Heinz Leonhard X.; Superti-Furga Giulio; Colinge Jacques; Bennett Keiryn L.
Source:: Journal of Proteome Research 2016 v.15 no.2 pp. 647-658
ISSN:: 1535-3907
Subject:: biotin; biotinylation; coatings; databases; drug therapy; drugs; liquid chromatography; mass spectrometry; membrane proteins; plasma membrane; prediction; proteome; proteomics; silica; swine; tunicamycin
Abstract:: ... Plasma membrane (PM) proteins contribute to the identity of a cell, mediate contact and communication, and account for more than two-thirds of known drug targets.1−8 In the past years, several protocols for the proteomic profiling of PM proteins have been described. Nevertheless, comparative analyses have mainly focused on different variations of one approach.9−11 We compared sulfo-NHS-SS-biotinyl ...
DOI:: 10.1021/acs.jproteome.5b01066
: https://doi.org/10.1021/acs.jproteome.5b01066

18. Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics

Author:: Jarnuczak Andrew F.; Lee Dave C. H.; Lawless Craig; Holman Stephen W.; Eyers Claire E.; Hubbard Simon J.
Source:: Journal of Proteome Research 2016 v.15 no.9 pp. 2945-2959
ISSN:: 1535-3907
Subject:: gases; hydrophobicity; ionization; ions; liquid chromatography; mass spectrometry; models; peptides; proteome; proteomics; yeasts
Abstract:: ... Quantitative mass spectrometry-based proteomics of complex biological samples remains challenging in part due to the variability and charge competition arising during electrospray ionization (ESI) of peptides and the subsequent transfer and detection of ions. These issues preclude direct quantification from signal intensity alone in the absence of a standard. A deeper understanding of the governin ...
DOI:: 10.1021/acs.jproteome.6b00048
: https://doi.org/10.1021/acs.jproteome.6b00048

19. BatMass: a Java Software Platform for LC–MS Data Visualization in Proteomics and Metabolomics

Author:: Avtonomov Dmitry M.; Raskind Alexander; Nesvizhskii Alexey I.
Source:: Journal of Proteome Research 2016 v.15 no.8 pp. 2500-2509
ISSN:: 1535-3907
Subject:: algorithms; brain; computer software; humans; information processing; liquid chromatography; mass spectrometry; metabolomics; proteome; proteomics; quality control
Abstract:: ... Mass spectrometry (MS) coupled to liquid chromatography (LC) is a commonly used technique in metabolomic and proteomic research. As the size and complexity of LC–MS-based experiments grow, it becomes increasingly more difficult to perform quality control of both raw data and processing results. In a practical setting, quality control steps for raw LC–MS data are often overlooked, and assessment of ...
DOI:: 10.1021/acs.jproteome.6b00021
PubMed:: 27306858
PubMed Central:: PMC5583644
: https://doi.org/10.1021/acs.jproteome.6b00021

20. Differential Isotope Labeling of Glycopeptides for Accurate Determination of Differences in Site-Specific Glycosylation

Author:: Pabst Martin; Benešová Iva; Fagerer Stephan R.; Jacobsen Mathias; Eyer Klaus; Schmidt Gregor; Steinhoff Robert; Krismer Jasmin; Wahl Fabian; Preisler Jan; Zenobi Renato
Source:: Journal of Proteome Research 2016 v.15 no.1 pp. 326-331
ISSN:: 1535-3907
Subject:: digestion; electrospray ionization mass spectrometry; glycopeptides; glycosylation; immunoglobulin G; isotope labeling; liquid chromatography; proteome; solid phase extraction; stable isotopes; trypsin
Abstract:: ... We introduce a stable isotope labeling approach for glycopeptides that allows a specific glycosylation site in a protein to be quantitatively evaluated using mass spectrometry. Succinic anhydride is used to specifically label primary amino groups of the peptide portion of the glycopeptides. The heavy form (D₄¹³C₄) provides an 8 Da mass increment over the light natural form (H₄¹²C₄), allowing simul ...
DOI:: 10.1021/acs.jproteome.5b00899
: https://doi.org/10.1021/acs.jproteome.5b00899

21. Discovery, Synthesis, and Functional Characterization of a Novel Neuroprotective Natural Product from the Fruit of Alpinia oxyphylla for use in Parkinson’s Disease Through LC/MS-Based Multivariate Data Analysis-Guided Fractionation

Author:: Li Guohui; Zhang Zaijun; Quan Quan; Jiang Renwang; Szeto Samuel S.W.; Yuan Shuai; Wong Wing-tak; Lam Herman H. C.; Lee Simon Ming-Yuen; Chu Ivan K.
Source:: Journal of Proteome Research 2016 v.15 no.8 pp. 2595-2606
ISSN:: 1535-3907
Subject:: Alpinia oxyphylla; Danio rerio; Parkinson disease; Western blotting; bioactive compounds; cerebellum; chemometrics; fractionation; ingredients; liquid chromatography; mass spectrometry; metabolomics; mice; neurons; neuroprotective effect; proteome; proteomics
Abstract:: ... Herein we report the discovery of a novel lead compound, oxyphylla A [(R)-4-(2-hydroxy-5-methylphenyl)-5-methylhexanoic acid] (from the fruit of Alpinia oxyphylla), which functions as a neuroprotective agent against Parkinson’s disease. To identify a shortlist of candidates from the extract of A. oxyphylla, we employed an integrated strategy combining liquid chromatography/mass spectrometry, bioac ...
DOI:: 10.1021/acs.jproteome.6b00152
: https://doi.org/10.1021/acs.jproteome.6b00152

22. Distinct Metabolic Signature of Human Bladder Cancer Cells Carrying an Impaired Fanconi Anemia Tumor-Suppressor Signaling Pathway

Author:: Panneerselvam Jayabal; Xie Guoxiang; Che Raymond; Su Mingming; Zhang Jun; Jia Wei; Fei Peiwen
Source:: Journal of Proteome Research 2016 v.15 no.4 pp. 1333-1341
ISSN:: 1535-3907
Subject:: Fanconi anemia; apoptosis; biomarkers; carcinogenesis; cell proliferation; gas chromatography-mass spectrometry; genomics; humans; liquid chromatography; metabolites; metabolomics; methionine; neoplasm cells; patients; phenylalanine; prognosis; proteome; signal transduction; threonine; urinary bladder neoplasms
Abstract:: ... Metabolic profiling has great potential to help the diagnosis and prognosis of cancer patients. Fanconi Anemia (FA) tumor-suppressor signaling has been instrumental in understanding human tumorigenesis. However, this instrumental understanding has never been demonstrated at the metabolic level. Here, we show that impaired FA signaling can lead cells to exhibit metabolic signatures of tumorigenesis ...
DOI:: 10.1021/acs.jproteome.6b00076
PubMed:: 26956768
PubMed Central:: PMC4874490
: https://doi.org/10.1021/acs.jproteome.6b00076

23. Fast and Reliable Quantitative Peptidomics with labelpepmatch

Author:: Verdonck Rik; De Haes Wouter; Cardoen Dries; Menschaert Gerben; Huhn Thomas; Landuyt Bart; Baggerman Geert; Boonen Kurt; Wenseleers Tom; Schoofs Liliane
Source:: Journal of Proteome Research 2016 v.15 no.3 pp. 1080-1089
ISSN:: 1535-3907
Subject:: Schistocerca gregaria; case studies; computer software; liquid chromatography; mass spectrometry; peptides; proteome; stable isotopes; statistical inference
Abstract:: ... The use of stable isotope tags in quantitative peptidomics offers many advantages, but the laborious identification of matching sets of labeled peptide peaks is still a major bottleneck. Here we present labelpepmatch, an R-package for fast and straightforward analysis of LC–MS spectra of labeled peptides. This open-source tool offers fast and accurate identification of peak pairs alongside an appr ...
DOI:: 10.1021/acs.jproteome.5b00845
: https://doi.org/10.1021/acs.jproteome.5b00845

24. Fecal Metabolome in Hmga1 Transgenic Mice with Polyposis: Evidence for Potential Screen for Early Detection of Precursor Lesions in Colorectal Cancer

Author:: Williams Michael D.; Xian Lingling; Huso Tait; Park Jeong-Jin; Huso David; Cope Leslie M.; Gang David R.; Siems William F.; Resar Linda; Reeves Raymond; Hill Herbert H.
Source:: Journal of Proteome Research 2016 v.15 no.12 pp. 4176-4187
ISSN:: 1535-3907
Subject:: bile acids; chromatin; colorectal neoplasms; fatty acids; feces; genes; humans; hypoxanthine; intestinal mucosa; liquid chromatography; mass spectrometry; metabolites; metabolome; mice; models; mortality; proteome; screening; taurine; transgenic animals; xanthine
Abstract:: ... Because colorectal cancer (CRC) remains a leading cause of cancer mortality worldwide, more accessible screening tests are urgently needed to identify early stage lesions. We hypothesized that highly sensitive, metabolic profile analysis of stool samples will identify metabolites associated with early stage lesions and could serve as a noninvasive screening test. We therefore applied traveling wav ...
DOI:: 10.1021/acs.jproteome.6b00035
: https://doi.org/10.1021/acs.jproteome.6b00035

25. High-Throughput LC–MS/MS Proteomic Analysis of a Mouse Model of Mesiotemporal Lobe Epilepsy Predicts Microglial Activation Underlying Disease Development

Author:: Bitsika Vasiliki; Duveau Venceslas; Simon-Areces Julia; Mullen William; Roucard Corinne; Makridakis Manousos; Mermelekas George; Savvopoulos Pantelis; Depaulis Antoine; Vlahou Antonia
Source:: Journal of Proteome Research 2016 v.15 no.5 pp. 1546-1562
ISSN:: 1535-3907
Subject:: animal models; astrocytes; epilepsy; humans; inflammation; liquid chromatography; mice; monitoring; neurodegenerative diseases; phenotype; protein synthesis; proteins; proteome; proteomics; synaptic transmission; tandem mass spectrometry
Abstract:: ... Uncovering the molecular mechanisms of mesiotemporal lobe epilepsy (MTLE) is critical to identify therapeutic targets. In this study, we performed global protein expression analysis of a kainic acid (KA) MTLE mouse model at various time-points (1, 3, and 30 days post-KA injection -dpi), representing specific stages of the syndrome. High-resolution liquid chromatography coupled to tandem mass spect ...
DOI:: 10.1021/acs.jproteome.6b00003
: https://doi.org/10.1021/acs.jproteome.6b00003

26. Immunoproteomics-Based Analysis of the Immunocompetent Serological Response to Lomentospora prolificans

Author:: Pellon Aize; Ramirez-Garcia Andoni; Buldain Idoia; Antoran Aitziber; Rementeria Aitor; Hernando Fernando L.
Source:: Journal of Proteome Research 2016 v.15 no.2 pp. 595-607
ISSN:: 1535-3907
Subject:: H+/K+-exchanging ATPase; H-transporting ATP synthase; antifungal agents; blood serum; conidia; diagnostic techniques; fungi; glyceraldehyde-3-phosphate dehydrogenase; heat shock proteins; humans; hyphae; immune response; immunocompromised population; immunodominant epitopes; immunoglobulin G; liquid chromatography; malate dehydrogenase; mortality; pathogens; phosphopyruvate hydratase; proteome; tandem mass spectrometry; virulence
Abstract:: ... The filamentous fungus Lomentospora prolificans is an emerging pathogen causing severe infections mainly among the immunocompromised population. These diseases course with high mortality rates due to great virulence of the fungus, its inherent resistance to available antifungals, and absence of specific diagnostic tools. Despite being widespread in humanized environments, L. prolificans rarely cau ...
DOI:: 10.1021/acs.jproteome.5b00978
: https://doi.org/10.1021/acs.jproteome.5b00978

27. Integrated Proteomic Pipeline Using Multiple Search Engines for a Proteogenomic Study with a Controlled Protein False Discovery Rate

Author:: Park Gun Wook; Hwang Heeyoun; Kim Kwang Hoe; Lee Ju Yeon; Lee Hyun Kyoung; Park Ji Yeong; Ji Eun Sun; Park Sung-Kyu Robin; Yates John R.; Kwon Kyung-Hoon; Park Young Mok; Lee Hyoung-Joo; Paik Young-Ki; Kim Jin Young; Yoo Jong Shin
Source:: Journal of Proteome Research 2016 v.15 no.11 pp. 4082-4090
ISSN:: 1535-3907
Subject:: alternative splicing; databases; humans; liquid chromatography; proteins; proteome; proteomics; synthetic peptides; tissues
Abstract:: ... In the Chromosome-Centric Human Proteome Project (C-HPP), false-positive identification by peptide spectrum matches (PSMs) after database searches is a major issue for proteogenomic studies using liquid-chromatography and mass-spectrometry-based large proteomic profiling. Here we developed a simple strategy for protein identification, with a controlled false discovery rate (FDR) at the protein lev ...
DOI:: 10.1021/acs.jproteome.6b00376
: https://doi.org/10.1021/acs.jproteome.6b00376

28. Nontargeted LC–MS Metabolomics Approach for Metabolic Profiling of Plasma and Urine from Pigs Fed Branched Chain Amino Acids for Maximum Growth Performance

Author:: Soumeh Elham A.; Hedemann Mette S.; Poulsen Hanne D.; Corrent Etienne; van Milgen Jacob; Nørgaard Jan V.
Source:: Journal of Proteome Research 2016 v.15 no.12 pp. 4195-4207
ISSN:: 1535-3907
Subject:: animal growth; ascorbic acid; biochemical pathways; blood; branched chain amino acids; choline; creatine; dose response; excretion; glycocholic acid; growth performance; hypoxanthine; liquid chromatography; mass spectrometry; metabolites; metabolomics; phenotype; proteome; swine; swine feeding; taurocholic acid; tyrosine; urine
Abstract:: ... The metabolic response in plasma and urine of pigs when feeding an optimum level of branched chain amino acids (BCAAs) for best growth performance is unknown. The objective of the current study was to identify the metabolic phenotype associated with the BCAAs intake level that could be linked to the animal growth performance. Three dose–response studies were carried out to collect blood and urine ...
DOI:: 10.1021/acs.jproteome.6b00184
: https://doi.org/10.1021/acs.jproteome.6b00184

29. Prediction of Protein Lysine Acylation by Integrating Primary Sequence Information with Multiple Functional Features

Author:: Du Yipeng; Zhai Zichao; Li Ying; Lu Ming; Cai Tanxi; Zhou Bo; Huang Lei; Wei Taotao; Li Tingting
Source:: Journal of Proteome Research 2016 v.15 no.12 pp. 4234-4244
ISSN:: 1535-3907
Subject:: Western blotting; acetylation; algorithms; correlation; data collection; gene ontology; liquid chromatography; lysine; mice; prediction; protein-protein interactions; proteins; proteome; proteomics; tandem mass spectrometry
Abstract:: ... Liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomic methods have been widely used to identify lysine acylation proteins. However, these experimental approaches often fail to detect proteins that are in low abundance or absent in specific biological samples. To circumvent these problems, we developed a computational method to predict lysine acylation, including acetylation, ma ...
DOI:: 10.1021/acs.jproteome.6b00240
: https://doi.org/10.1021/acs.jproteome.6b00240

30. Proteome Differences between Hepatitis B Virus Genotype-B- and Genotype-C-Induced Hepatocellular Carcinoma Revealed by iTRAQ-Based Quantitative Proteomics

Author:: Wei Dahai; Zeng Yongyi; Xing Xiaohua; Liu Hongzhi; Lin Minjie; Han Xiao; Liu Xiaolong; Liu Jingfeng
Source:: Journal of Proteome Research 2016 v.15 no.2 pp. 487-498
ISSN:: 1535-3907
Subject:: Hepatitis B virus; biomarkers; carcinogenesis; genotype; hepatoma; liquid chromatography; proteins; proteome; proteomics; tandem mass spectrometry; tissues; viruses; South East Asia
Abstract:: ... Hepatitis B virus (HBV) is the main cause of hepatocellular carcinoma (HCC) in southeast Asia where HBV genotype B and genotype C are the most prevalent. Viral genotypes have been reported to significantly affect the clinical outcomes of HCC. However, the underlying molecular differences among different genotypes of HBV virus infected HCC have not been revealed. Here, we applied isobaric tags for ...
DOI:: 10.1021/acs.jproteome.5b00838
: https://doi.org/10.1021/acs.jproteome.5b00838

31. Proteomic Analysis of Human Tendon and Ligament: Solubilization and Analysis of Insoluble Extracellular Matrix in Connective Tissues

Author:: Sato Nori; Taniguchi Takako; Goda Yuichiro; Kosaka Hirofumi; Higashino Kosaku; Sakai Toshinori; Katoh Shinsuke; Yasui Natsuo; Sairyo Koichi; Taniguchi Hisaaki
Source:: Journal of Proteome Research 2016 v.15 no.12 pp. 4709-4721
ISSN:: 1535-3907
Subject:: cartilage; crosslinking; digestion; elastase; extracellular matrix; humans; ligaments; liquid chromatography; mass spectrometry; pathophysiology; peptides; proteins; proteome; proteomics; quantitative analysis; solubilization
Abstract:: ... Connective tissues such as tendon, ligament and cartilage are mostly composed of extracellular matrix (ECM). These tissues are insoluble, mainly due to the highly cross-linked ECM proteins such as collagens. Difficulties obtaining suitable samples for mass spectrometric analysis render the application of modern proteomic technologies difficult. Complete solubilization of them would not only elucid ...
DOI:: 10.1021/acs.jproteome.6b00806
: https://doi.org/10.1021/acs.jproteome.6b00806

32. Proteomics Quality Control: Quality Control Software for MaxQuant Results

Author:: Bielow Chris; Mastrobuoni Guido; Kempa Stefan
Source:: Journal of Proteome Research 2016 v.15 no.3 pp. 777-787
ISSN:: 1535-3907
Subject:: amino acids; cell culture; computer software; experimental design; isotope labeling; liquid chromatography; mass spectrometry; proteome; proteomics; quality control; stable isotopes
Abstract:: ... Mass spectrometry-based proteomics coupled to liquid chromatography has matured into an automatized, high-throughput technology, producing data on the scale of multiple gigabytes per instrument per day. Consequently, an automated quality control (QC) and quality analysis (QA) capable of detecting measurement bias, verifying consistency, and avoiding propagation of error is paramount for instrument ...
DOI:: 10.1021/acs.jproteome.5b00780
: https://doi.org/10.1021/acs.jproteome.5b00780

33. Targeted Metabolomic Pathway Analysis and Validation Revealed Glutamatergic Disorder in the Prefrontal Cortex among the Chronic Social Defeat Stress Mice Model of Depression

Author:: Wang Wei; Guo Hua; Zhang Shu-Xiao; Li Juan; Cheng Ke; Bai Shun-Jie; Yang De-Yu; Wang Hai-Yang; Liang Zi-Hong; Liao Li; Sun Lin; Xie Peng
Source:: Journal of Proteome Research 2016 v.15 no.10 pp. 3784-3792
ISSN:: 1535-3907
Subject:: L-dopa; Western blotting; animal models; cortex; glutamic acid; liquid chromatography; mental depression; metabolites; metabolomics; mice; pathogenesis; perfluorocarbons; phenotype; prefrontal cortex; proteome; quality of life; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; risk factors; tandem mass spectrometry
Abstract:: ... Major depressive disorder (MDD) is a severe psychiatric disease that has critically affected life quality for millions of people. Chronic stress is gradually recognized as a primary pathogenesis risk factor of MDD. Despite the remarkable progress in mechanism research, the pathogenesis mechanism of MDD is still not well understood. Therefore, we conducted a liquid chromatography–tandem mass spectr ...
DOI:: 10.1021/acs.jproteome.6b00577
: https://doi.org/10.1021/acs.jproteome.6b00577

34. A Method for Comprehensive Glycosite-Mapping and Direct Quantitation of Serum Glycoproteins

Author:: Hong Qiuting; Ruhaak L. Renee; Stroble Carol; Parker Evan; Huang Jincui; Maverakis Emanual; Lebrilla Carlito B.
Source:: Journal of Proteome Research 2015 v.14 no.12 pp. 5179-5192
ISSN:: 1535-3907
Subject:: biomarkers; blood serum; computer software; glycopeptides; glycoproteins; glycosylation; humans; immunoglobulin A; immunoglobulin G; immunoglobulin M; liquid chromatography; mass spectrometry; monitoring; polysaccharides; protein content; proteome
Abstract:: ... A comprehensive glycan map was constructed for the top eight abundant glycoproteins in plasma using both specific and nonspecific enzyme digestions followed by nano liquid chromatography (LC)–chip/quadrupole time-of-flight mass spectrometry (MS) analysis. Glycopeptides were identified using an in-house software tool, GPFinder. A sensitive and reproducible multiple reaction monitoring (MRM) techniq ...
DOI:: 10.1021/acs.jproteome.5b00756
PubMed:: 26510530
PubMed Central:: PMC4670571
: https://doi.org/10.1021/acs.jproteome.5b00756

35. ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments

Author:: Choi Meena; Eren-Dogu Zeynep F.; Colangelo Christopher; Cottrell John; Hoopmann Michael R.; Kapp Eugene A.; Kim Sangtae; Lam Henry; Neubert Thomas A.; Palmblad Magnus; Phinney Brett S.; Weintraub Susan T.; MacLean Brendan; Vitek Olga
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 945-957
ISSN:: 1535-3907
Subject:: computer software; data collection; liquid chromatography; proteins; proteome; statistical analysis; tandem mass spectrometry; uncertainty
Abstract:: ... Detection of differentially abundant proteins in label-free quantitative shotgun liquid chromatography–tandem mass spectrometry (LC–MS/MS) experiments requires a series of computational steps that identify and quantify LC–MS features. It also requires statistical analyses that distinguish systematic changes in abundance between conditions from artifacts of biological and technical variation. The 2 ...
DOI:: 10.1021/acs.jproteome.6b00881
: https://doi.org/10.1021/acs.jproteome.6b00881

36. Antibiotic Treatment Preventing Necrotising Enterocolitis Alters Urinary and Plasma Metabolomes in Preterm Pigs

Author:: Jiang Pingping; Trimigno Alessia; Stanstrup Jan; Khakimov Bekzod; Viereck Nanna; Engelsen Søren Balling; Sangild Per Torp; Dragsted Lars Ove
Source:: Journal of Proteome Research 2017 v.16 no.10 pp. 3547-3557
ISSN:: 1535-3907
Subject:: antibiotics; bile acids; digestive system; enterocolitis; intestinal microorganisms; kynurenine pathway; liquid chromatography; mass spectrometry; metabolism; metabolites; metabolome; models; neonates; nuclear magnetic resonance spectroscopy; phenylalanine; premature birth; proteome; serotonin; swine; tryptophan
Abstract:: ... Necrotising enterocolitis (NEC) is a serious gut inflammatory condition in premature neonates, onset and development of which depend on the gut microbiome. Attenuation of the gut microbiome by antibiotics can reduce NEC incidence and severity. However, how the antibiotics-suppressed gut microbiome affects the whole-body metabolism in NEC-sensitive premature neonates is unknown. In formula-fed pret ...
DOI:: 10.1021/acs.jproteome.7b00263
: https://doi.org/10.1021/acs.jproteome.7b00263

37. Attached and Planktonic Listeria monocytogenes Global Proteomic Responses and Associated Influence of Strain Genetics and Temperature

Author:: Mata Marcia M.; da Silva Wladimir P.; Wilson Richard; Lowe Edwin; Bowman John P.
Source:: Journal of Proteome Research 2015 v.14 no.2 pp. 1161-1173
ISSN:: 1535-3907
Subject:: Listeria monocytogenes; biosynthesis; environmental fate; food pathogens; liquid chromatography; polymers; proteome; proteomics; strain differences; stress response; surface proteins; tandem mass spectrometry; temperature
Abstract:: ... Contamination of industrial and domestic food usage environments by the attachement of bacterial food-borne pathogen Listeria monocytogenes has public health and economic implications. Comprehensive proteomics experiments using label-free liquid chromatography/tandem mass spectrometry were used to compare the proteomes of two different L. monocytogenes strains (Siliken_1/2c and F2365_4b), which sh ...
DOI:: 10.1021/pr501114e
: https://doi.org/10.1021/pr501114e

38. Branched-Chain Amino Acids as Predictors for Individual Differences of Cisplatin Nephrotoxicity in Rats: A Pharmacometabonomics Study

Author:: Zhang Pei; Li Wei; Chen Jiaqing; Li Ruiting; Zhang Zunjian; Huang Yin; Xu Fengguo
Source:: Journal of Proteome Research 2017 v.16 no.4 pp. 1753-1762
ISSN:: 1535-3907
Subject:: adverse effects; amino acids; biomedical research; blood serum; cisplatin; clinical trials; graphs; liquid chromatography; medicine; metabolomics; nephrotoxicity; proteome; rats; regression analysis; tandem mass spectrometry
Abstract:: ... Nephrotoxicity is the dose-limiting adverse effect of cisplatin with large individual differences. Up to now, little has been done on how to recognize and predict the individual differences in either preclinical or clinical research. In the present study, important postdose indicators were screened out first and integrated into a grouping factor, according to which rats were recognized as lowly or ...
DOI:: 10.1021/acs.jproteome.7b00014
: https://doi.org/10.1021/acs.jproteome.7b00014

39. Cartilaginous Metabolomic Study Reveals Potential Mechanisms of Osteophyte Formation in Osteoarthritis

Author:: Xu Zhongwei; Chen Tingmei; Luo Jiao; Ding Shijia; Gao Sichuan; Zhang Jian
Source:: Journal of Proteome Research 2017 v.16 no.4 pp. 1425-1435
ISSN:: 1535-3907
Subject:: discriminant analysis; metabolism; proteome; osteoarthritis; models; least squares; collagen; bone formation; cartilage; sulfonic acids; phenylalanine; pathogenesis; mass spectrometry; liquid chromatography; metabolomics; metabolites
Abstract:: ... Osteophyte is one of the inevitable consequences of progressive osteoarthritis with the main characteristics of cartilage degeneration and endochondral ossification. The pathogenesis of osteophyte formation is not fully understood to date. In this work, metabolomic approaches were employed to explore potential mechanisms of osteophyte formation by detecting metabolic variations between extracts of ...
DOI:: 10.1021/acs.jproteome.6b00676
: https://doi.org/10.1021/acs.jproteome.6b00676

40. Characterization of the Molecular Mechanisms Underlying the Chronic Phase of Stroke in a Cynomolgus Monkey Model of Induced Cerebral Ischemia

Author:: Law Henry C. H.; Szeto Samuel S. W.; Quan Quan; Zhao Yun; Zhang Zaijun; Krakovska Olga; Lui Leong Ting; Zheng Chengyou; Lee Simon M.-Y.; Siu K. W. Michael; Wang Yuqiang; Chu Ivan K.
Source:: Journal of Proteome Research 2017 v.16 no.3 pp. 1150-1166
ISSN:: 1535-3907
Subject:: Macaca fascicularis; cerebral cortex; cytoskeleton; infarction; inflammation; ischemia; liquid chromatography; models; mortality; neurogenesis; proteins; proteome; proteomics; stroke; synaptogenesis
Abstract:: ... Stroke is one of the main causes of mortality and long-term disability worldwide. The pathophysiological mechanisms underlying this disease are not well understood, particularly in the chronic phase after the initial ischemic episode. In this study, a Macaca fascicularis stroke model consisting of two sample groups, as determined by MRI-quantified infarct volumes as a measure of the stroke severit ...
DOI:: 10.1021/acs.jproteome.6b00651
: https://doi.org/10.1021/acs.jproteome.6b00651

41. Combining De Novo Peptide Sequencing Algorithms, A Synergistic Approach to Boost Both Identifications and Confidence in Bottom-up Proteomics

Author:: Blank-Landeshammer Bernhard; Kollipara Laxmikanth; Biß Karsten; Pfenninger Markus; Malchow Sebastian; Shuvaev Konstantin; Zahedi René P.; Sickmann Albert
Source:: Journal of Proteome Research 2017 v.16 no.9 pp. 3209-3218
ISSN:: 1535-3907
Subject:: algorithms; data collection; databases; digestion; liquid chromatography; mass spectrometry; peptides; proteome; proteomics
Abstract:: ... Complex mass spectrometry based proteomics data sets are mostly analyzed by protein database searches. While this approach performs considerably well for sequenced organisms, direct inference of peptide sequences from tandem mass spectra, i.e., de novo peptide sequencing, oftentimes is the only way to obtain information when protein databases are absent. However, available algorithms suffer from d ...
DOI:: 10.1021/acs.jproteome.7b00198
: https://doi.org/10.1021/acs.jproteome.7b00198

42. Comparative Proteomic Analysis of Developing Rhizomes of the Ancient Vascular Plant Equisetum hyemale and Different Monocot Species

Author:: Salvato Fernanda; Balbuena Tiago S.; Nelson William; Rao R. Shyama Prasad; He Ruifeng; Soderlund Carol A.; Gang David R.; Thelen Jay J.
Source:: Journal of Proteome Research 2015 v.14 no.4 pp. 1779-1791
ISSN:: 1535-3907
Subject:: Equisetum hyemale; Liliopsida; biomass; electrophoresis; forage; fuel production; grasses; liquid chromatography; metabolism; proteins; proteome; proteomics; rhizomes; tandem mass spectrometry
Abstract:: ... The rhizome is responsible for the invasiveness and competitiveness of many plants with great economic and agricultural impact worldwide. Besides its value as an invasive organ, the rhizome plays a role in the establishment and massive growth of forage, providing biomass for biofuel production. Despite these features, little is known about the molecular mechanisms that contribute to rhizome growth ...
DOI:: 10.1021/pr501157w
: https://doi.org/10.1021/pr501157w

43. Comparative Proteomic Analysis of Wild-Type and SAP Domain Mutant Foot-and-Mouth Disease Virus-Infected Porcine Cells Identifies the Ubiquitin-Activating Enzyme UBE1 Required for Virus Replication

Author:: Zhu Zixiang; Yang Fan; Zhang Keshan; Cao Weijun; Jin Ye; Wang Guoqing; Mao Ruoqing; Li Dan; Guo Jianhong; Liu Xiangtao; Zheng Haixue
Source:: Journal of Proteome Research 2015 v.14 no.10 pp. 4194-4206
ISSN:: 1535-3907
Subject:: Foot-and-mouth disease virus; electrospray ionization mass spectrometry; foot-and-mouth disease; interferons; liquid chromatography; mutants; pathogenicity; protein domains; proteome; proteomics; ribosomes; signal transduction; spliceosomes; swine; transactivators; ubiquitin-protein ligase; virus replication
Abstract:: ... Leader protein (Lᵖʳᵒ) of foot-and-mouth disease virus (FMDV) manipulates the activities of several host proteins to promote viral replication and pathogenicity. Lᵖʳᵒ has a conserved protein domain SAP that is suggested to subvert interferon (IFN) production to block antiviral responses. However, apart from blocking IFN production, the roles of the SAP domain during FMDV infection in host cells rem ...
DOI:: 10.1021/acs.jproteome.5b00310
: https://doi.org/10.1021/acs.jproteome.5b00310

44. Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra

Author:: Rieder Vera; Schork Karin U.; Kerschke Laura; Blank-Landeshammer Bernhard; Sickmann Albert; Rahnenführer Jörg
Source:: Journal of Proteome Research 2017 v.16 no.11 pp. 4035-4044
ISSN:: 1535-3907
Subject:: algorithms; data collection; databases; liquid chromatography; peptides; proteins; proteome; proteomics; quality control; tandem mass spectrometry
Abstract:: ... In proteomics, liquid chromatography–tandem mass spectrometry (LC–MS/MS) is established for identifying peptides and proteins. Duplicated spectra, that is, multiple spectra of the same peptide, occur both in single MS/MS runs and in large spectral libraries. Clustering tandem mass spectra is used to find consensus spectra, with manifold applications. First, it speeds up database searches, as perfo ...
DOI:: 10.1021/acs.jproteome.7b00427
: https://doi.org/10.1021/acs.jproteome.7b00427

45. Comprehensive Metabolic Profiling of Age-Related Mitochondrial Dysfunction in the High-Fat-Fed ob/ob Mouse Heart

Author:: Wang Xinzhu; West James A.; Murray Andrew J.; Griffin Julian L.
Source:: Journal of Proteome Research 2015 v.14 no.7 pp. 2849-2862
ISSN:: 1535-3907
Subject:: cardiomyopathy; diacylglycerols; diet; heart; lipotoxicity; liquid chromatography; mass spectrometry; metabolomics; mice; mitochondria; oxidative stress; proteome; triacylglycerols
Abstract:: ... The ectopic deposition of fat is thought to lead to lipotoxicity and has been associated with mitochondrial dysfunction and diabetic cardiomyopathy. We have measured mitochondrial respiratory capacities in the hearts of ob/ob and wild-type mice on either a regular chow (RCD) or high-fat (HFD) diet across four age groups to investigate the impact of diet and age on mitochondrial function alongside ...
DOI:: 10.1021/acs.jproteome.5b00128
: https://doi.org/10.1021/acs.jproteome.5b00128

46. DIGESTIF: A Universal Quality Standard for the Control of Bottom-Up Proteomics Experiments

Author:: Lebert Dorothée; Louwagie Mathilde; Goetze Sandra; Picard Guillaume; Ossola Reto; Duquesne Caroline; Basler Konrad; Ferro Myriam; Rinner Oliver; Aebersold Ruedi; Garin Jérôme; Mouz Nicolas; Brunner Erich; Brun Virginie
Source:: Journal of Proteome Research 2015 v.14 no.2 pp. 787-803
ISSN:: 1535-3907
Subject:: amino acids; biomarkers; ionization; liquid chromatography; mass spectrometry; peptides; proteinases; proteolysis; proteome; proteomics; recombinant proteins; scaffolding proteins; screening
Abstract:: ... In bottom-up mass spectrometry-based proteomics analyses, variability at any step of the process, particularly during sample proteolysis, directly affects the sensitivity, accuracy, and precision of peptide detection and quantification. Currently, no generic internal standards are available to control the quality of sample processing steps. This makes it difficult to assess the comparability of MS ...
DOI:: 10.1021/pr500834z
: https://doi.org/10.1021/pr500834z

47. Deep Phosphotyrosine Proteomics by Optimization of Phosphotyrosine Enrichment and MS/MS Parameters

Author:: Abe Yuichi; Nagano Maiko; Tada Asa; Adachi Jun; Tomonaga Takeshi
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 1077-1086
ISSN:: 1535-3907
Subject:: carcinogenesis; databases; enzyme inhibitors; epidermal growth factor receptors; liquid chromatography; phosphorylation; post-translational modification; proteome; proteomics; tandem mass spectrometry; tyrosine
Abstract:: ... Phosphorylation is a major post-translational modification that regulates protein function, with phosphotyrosine (pY) modifications being implicated in oncogenesis. However, global profiling of pY statuses without treatment with a tyrosine phosphatase inhibitor such as pervanadate is still challenging due to the low occupancy of pY sites. In this study, we greatly improved the identification of pY ...
DOI:: 10.1021/acs.jproteome.6b00576
: https://doi.org/10.1021/acs.jproteome.6b00576

48. Development of Urinary Pseudotargeted LC-MS-Based Metabolomics Method and Its Application in Hepatocellular Carcinoma Biomarker Discovery

Author:: Shao Yaping; Zhu Bin; Zheng Ruiyin; Zhao Xinjie; Yin Peiyuan; Lu Xin; Jiao Binghua; Xu Guowang; Yao Zhenzhen
Source:: Journal of Proteome Research 2015 v.14 no.2 pp. 906-916
ISSN:: 1535-3907
Subject:: bile acids; biomarkers; carnitine; citric acid; cyclic AMP; death; energy metabolism; glutamine; hepatoma; liquid chromatography; mass spectrometry; metabolites; metabolomics; nucleosides; regression analysis
Abstract:: ... Hepatocellular carcinoma (HCC) is one of the pestilent malignancies leading to cancer-related death. Discovering effective biomarkers for HCC diagnosis is an urgent demand. To identify potential metabolite biomarkers, we developed a urinary pseudotargeted method based on liquid chromatography–hybrid triple quadrupole linear ion trap mass spectrometry (LC–QTRAP MS). Compared with nontargeted method ...
DOI:: 10.1021/pr500973d
: https://doi.org/10.1021/pr500973d

49. Development of a Postcolumn Infused-Internal Standard Liquid Chromatography Mass Spectrometry Method for Quantitative Metabolomics Studies

Author:: Liao Hsiao-Wei; Chen Guan-Yuan; Wu Ming-Shiang; Liao Wei-Chih; Lin Ching-Hung; Kuo Ching-Hua
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 1097-1104
ISSN:: 1535-3907
Subject:: biomedical research; breast neoplasms; electrospray ionization mass spectrometry; liquid chromatography; liquids; metabolites; metabolomics; patients; principal component analysis; proteome; tryptophan
Abstract:: ... Quantitative metabolomics has become much more important in clinical research in recent years. Individual differences in matrix effects (MEs) and the injection order effect are two major factors that reduce the quantification accuracy in liquid chromatography–electrospray ionization–mass spectrometry-based (LC–ESI–MS) metabolomics studies. This study proposed a postcolumn infused-internal standard ...
DOI:: 10.1021/acs.jproteome.6b01011
: https://doi.org/10.1021/acs.jproteome.6b01011

50. Differential Peptide Labeling (iTRAQ) in LC–MS/MS Based Proteomics in Daphnia Reveal Mechanisms of an Antipredator Response

Author:: Effertz Christoph; Müller Stefan; Elert Eric von
Source:: Journal of Proteome Research 2015 v.14 no.2 pp. 888-896
ISSN:: 1535-3907
Subject:: Daphnia; antipredatory behavior; fish; kairomones; life history; liquid chromatography; models; predator-prey relationships; predators; proteins; proteome; proteomics; tandem mass spectrometry
Abstract:: ... Daphnia, an important model organism for studies on ecology and evolution, has become a textbook example for inducible defenses against predators. Inducible defenses are widespread in nature, and the underlying molecular mechanisms for this plasticity in general and in particular in Daphnia are not fully understood. Here, we provide for the first time a combination of established life-history chan ...
DOI:: 10.1021/pr500948a
: https://doi.org/10.1021/pr500948a

51. Experimental Null Method to Guide the Development of Technical Procedures and to Control False-Positive Discovery in Quantitative Proteomics

Author:: Shen Xiaomeng; Hu Qiang; Li Jun; Wang Jianmin; Qu Jun
Source:: Journal of Proteome Research 2015 v.14 no.10 pp. 4147-4157
ISSN:: 1535-3907
Subject:: biomarkers; experimental design; information processing; liquid chromatography; mass spectrometry; proteins; proteome; proteomics; quantitative analysis
Abstract:: ... Comprehensive and accurate evaluation of data quality and false-positive biomarker discovery is critical to direct the method development/optimization for quantitative proteomics, which nonetheless remains challenging largely due to the high complexity and unique features of proteomic data. Here we describe an experimental null (EN) method to address this need. Because the method experimentally me ...
DOI:: 10.1021/acs.jproteome.5b00200
PubMed:: 26051676
PubMed Central:: PMC5905339
: https://doi.org/10.1021/acs.jproteome.5b00200

52. Forecasting Chronic Diseases Using Data Fusion

Author:: Acar Evrim; Gürdeniz Gözde; Savorani Francesco; Hansen Louise; Olsen Anja; Tjønneland Anne; Dragsted Lars Ove; Bro Rasmus
Source:: Journal of Proteome Research 2017 v.16 no.7 pp. 2435-2444
ISSN:: 1535-3907
Subject:: artificial intelligence; biomarkers; breast neoplasms; chronic diseases; colorectal neoplasms; data collection; lifestyle; liquid chromatography; mass spectrometry; metabolites; metabolomics; models; nuclear magnetic resonance spectroscopy; proteome
Abstract:: ... Data fusion, that is, extracting information through the fusion of complementary data sets, is a topic of great interest in metabolomics because analytical platforms such as liquid chromatography–mass spectrometry (LC–MS) and nuclear magnetic resonance (NMR) spectroscopy commonly used for chemical profiling of biofluids provide complementary information. In this study, with a goal of forecasting a ...
DOI:: 10.1021/acs.jproteome.7b00039
: https://doi.org/10.1021/acs.jproteome.7b00039

53. Francisella tularensis LVS Surface and Membrane Proteins as Targets of Effective Post-Exposure Immunization for Tularemia

Author:: Chandler Jeffrey C.; Sutherland Marjorie D.; Harton Marisa R.; Molins Claudia R.; Anderson Rebecca V.; Heaslip Darragh G.; Bosio Catharine M.; Belisle John T.
Source:: Journal of Proteome Research 2015 v.14 no.2 pp. 664-675
ISSN:: 1535-3907
Subject:: Francisella tularensis; Western blotting; antibiotics; antigens; antiserum; bioinformatics; immunization; liquid chromatography; membrane proteins; mice; prioritization; protein composition; proteome; proteomics; surface proteins; tandem mass spectrometry; tularemia; vaccine development
Abstract:: ... Francisella tularensis causes disease (tularemia) in a large number of mammals, including man. We previously demonstrated enhanced efficacy of conventional antibiotic therapy for tularemia by postexposure passive transfer of immune sera developed against a F. tularensis LVS membrane protein fraction (MPF). However, the protein composition of this immunogenic fraction was not defined. Proteomic app ...
DOI:: 10.1021/pr500628k
PubMed:: 25494920
PubMed Central:: PMC4324441
: https://doi.org/10.1021/pr500628k

54. Gas Chromatography/Mass Spectrometry Metabolomics of Urine and Serum from Nonhuman Primates Exposed to Ionizing Radiation: Impacts on the Tricarboxylic Acid Cycle and Protein Metabolism

Author:: Pannkuk Evan L.; Laiakis Evagelia C.; Authier Simon; Wong Karen; Fornace Albert J.
Source:: Journal of Proteome Research 2017 v.16 no.5 pp. 2091-2100
ISSN:: 1535-3907
Subject:: Primates; accidents; amino acid metabolism; biomarkers; blood serum; carboxylic acids; complications (disease); death; equipment; free radicals; gas chromatography; inflammation; ionizing radiation; isomers; liquid chromatography; mass spectrometry; metabolites; metabolomics; microorganisms; multivariate analysis; neoplasms; proteome; radioactive waste; rapid methods; tissues; tricarboxylic acid cycle; urine
Abstract:: ... Ionizing radiation (IR) directly damages cells and tissues or indirectly damages them through reactive free radicals that may lead to longer term adverse sequelae such as cancers, persistent inflammation, or possible death. Potential exposures include nuclear reactor accidents, improper disposal of equipment containing radioactive materials or medical errors, and terrorist attacks. Metabolomics (c ...
DOI:: 10.1021/acs.jproteome.7b00064
PubMed:: 28351153
PubMed Central:: PMC5720681
: https://doi.org/10.1021/acs.jproteome.7b00064

55. Glycoproteins in Claudin-Low Breast Cancer Cell Lines Have a Unique Expression Profile

Author:: Yen Ten-Yang; Bowen Spencer; Yen Roger; Piryatinska Alexandra; Macher Bruce A.; Timpe Leslie C.
Source:: Journal of Proteome Research 2017 v.16 no.4 pp. 1391-1400
ISSN:: 1535-3907
Subject:: breast neoplasms; breasts; cell lines; epithelium; estrogen receptors; gene expression; genes; glycoproteins; liquid chromatography; messenger RNA; patients; protein synthesis; proteome; proteomics; tandem mass spectrometry; tight junctions
Abstract:: ... Claudin proteins are components of epithelial tight junctions; a subtype of breast cancer has been defined by the reduced expression of mRNA for claudins and other genes. Here, we characterize the expression of glycoproteins in breast cell lines for the claudin-low subtype using liquid chromatography/tandem mass spectrometry. Unsupervised clustering techniques reveal a group of claudin-low cell li ...
DOI:: 10.1021/acs.jproteome.6b00470
PubMed:: 28287265
PubMed Central:: PMC5557415
: https://doi.org/10.1021/acs.jproteome.6b00470

56. Glycoproteomic Comparison of Clinical Triple-Negative and Luminal Breast Tumors

Author:: Hill Jennifer J.; Tremblay Tammy-Lynn; Fauteux François; Li Jie; Wang Edwin; Aguilar-Mahecha Adriana; Basik Mark; O’Connor-McCourt Maureen
Source:: Journal of Proteome Research 2015 v.14 no.3 pp. 1376-1388
ISSN:: 1535-3907
Subject:: Western blotting; breast neoplasms; erbB-2 receptor; estrogens; gene expression; gene expression regulation; hormone replacement therapy; liquid chromatography; mass spectrometry; messenger RNA; microarray technology; patients; progesterone receptors; prognosis; protein synthesis; proteome; relapse
Abstract:: ... Triple-negative (TN) breast cancer accounts for ∼15% of breast cancers and is characterized by a high likelihood of relapse and a lack of targeted therapies. In contrast, luminal-type tumors that express the estrogen and progesterone receptors (ER+/PR+) and lack expression of human epidermal growth factor receptor 2 (Her2−) are treated with targeted hormonal therapy and carry a better prognosis. T ...
DOI:: 10.1021/pr500987r
: https://doi.org/10.1021/pr500987r

57. Hippocampal Proteomic and Metabonomic Abnormalities in Neurotransmission, Oxidative Stress, and Apoptotic Pathways in a Chronic Phencyclidine Rat Model

Author:: Wesseling Hendrik; Want Elizabeth J.; Guest Paul C.; Rahmoune Hassan; Holmes Elaine; Bahn Sabine
Source:: Journal of Proteome Research 2015 v.14 no.8 pp. 3174-3187
ISSN:: 1535-3907
Subject:: animal models; antagonism; apoptosis; bioinformatics; blood serum; disease models; drugs; fibroblast growth factor 2; frontal lobe; glutamate receptors; hippocampus; immunoassays; interleukin-1beta; interleukin-2; interleukin-5; liquid chromatography; mass spectrometry; metabolomics; monitoring; neurodegenerative diseases; neurotransmitters; oxidative stress; patients; proteome; proteomics; schizophrenia; superoxide dismutase; tissues
Abstract:: ... Schizophrenia is a neuropsychiatric disorder affecting 1% of the world’s population. Due to both a broad range of symptoms and disease heterogeneity, current therapeutic approaches to treat schizophrenia fail to address all symptomatic manifestations of the disease. Therefore, disease models that reproduce core pathological features of schizophrenia are needed for the elucidation of pathological d ...
DOI:: 10.1021/acs.jproteome.5b00105
: https://doi.org/10.1021/acs.jproteome.5b00105

58. Identification of Proteomic Features To Distinguish Benign Pulmonary Nodules from Lung Adenocarcinoma

Author:: Codreanu Simona G.; Hoeksema Megan D.; Slebos Robbert J. C.; Zimmerman Lisa J.; Rahman S. M. Jamshedur; Li Ming; Chen Sheau-Chiann; Chen Heidi; Eisenberg Rosana; Liebler Daniel C.; Massion Pierre P.
Source:: Journal of Proteome Research 2017 v.16 no.9 pp. 3266-3276
ISSN:: 1535-3907
Subject:: adenocarcinoma; biomarkers; biopsy; chemokine CCL19; epithelium; immunohistochemistry; liquid chromatography; lungs; microarray technology; monitoring; protein synthesis; proteins; proteome; proteomics; tandem mass spectrometry
Abstract:: ... We hypothesized that distinct protein expression features of benign and malignant pulmonary nodules may reveal novel candidate biomarkers for the early detection of lung cancer. We performed proteome profiling by liquid chromatography–tandem mass spectrometry to characterize 34 resected benign lung nodules, 24 untreated lung adenocarcinomas (ADCs), and biopsies of bronchial epithelium. Group compa ...
DOI:: 10.1021/acs.jproteome.7b00245
PubMed:: 28731711
PubMed Central:: PMC6339813
: https://doi.org/10.1021/acs.jproteome.7b00245

59. Kinobead and Single-Shot LC-MS Profiling Identifies Selective PKD Inhibitors

Author:: Golkowski Martin; Vidadala Rama Subba Rao; Lombard Chloe K.; Suh Hyong Won; Maly Dustin J.; Ong Shao-En
Source:: Journal of Proteome Research 2017 v.16 no.3 pp. 1216-1227
ISSN:: 1535-3907
Subject:: active sites; cell lines; digestion; enzyme inhibitors; humans; liquid chromatography; mass spectrometry; mechanism of action; monitoring; neoplasms; protein kinases; proteome
Abstract:: ... ATP-competitive protein kinase inhibitors are important research tools and therapeutic agents. Because there are >500 human kinases that contain highly conserved active sites, the development of selective inhibitors is extremely challenging. Methods to rapidly and efficiently profile kinase inhibitor targets in cell lysates are urgently needed to discover selective compounds and to elucidate the m ...
DOI:: 10.1021/acs.jproteome.6b00817
PubMed:: 28102076
PubMed Central:: PMC5663466
: https://doi.org/10.1021/acs.jproteome.6b00817

60. LC–MS Metabolomics of Psoriasis Patients Reveals Disease Severity-Dependent Increases in Circulating Amino Acids That Are Ameliorated by Anti-TNFα Treatment

Author:: Kamleh Muhammad Anas; Snowden Stuart G.; Grapov Dmitry; Blackburn Gavin J.; Watson David G.; Xu Ning; Ståhle Mona; Wheelock Craig E.
Source:: Journal of Proteome Research 2015 v.14 no.1 pp. 557-566
ISSN:: 1535-3907
Subject:: alanine; arginine; aspartic acid; biochemical pathways; cachexia; collagen; drugs; environmental factors; epidemiological studies; glutamic acid; keratinocytes; liquid chromatography; mass spectrometry; metabolites; metabolomics; monitoring; patients; phenotype; proline; psoriasis; serine; threonine
Abstract:: ... Psoriasis is an immune-mediated highly heterogeneous skin disease in which genetic as well as environmental factors play important roles. In spite of the local manifestations of the disease, psoriasis may progress to affect organs deeper than the skin. These effects are documented by epidemiological studies, but they are not yet mechanistically understood. In order to provide insight into the syst ...
DOI:: 10.1021/pr500782g
PubMed:: 25361234
PubMed Central:: PMC4286171
: https://doi.org/10.1021/pr500782g

61. Metabonomic Profiling Reveals Cancer Chemopreventive Effects of American Ginseng on Colon Carcinogenesis in ApcMin/+ Mice

Author:: Xie Guoxiang; Wang Chong-Zhi; Yu Chunhao; Qiu Yunping; Wen Xiao-Dong; Zhang Chun-Feng; Yuan Chun-Su; Jia Wei
Source:: Journal of Proteome Research 2015 v.14 no.8 pp. 3336-3347
ISSN:: 1535-3907
Subject:: Panax quinquefolius; animal models; antineoplastic activity; antioxidants; arachidonic acid; carcinogenesis; chemoprevention; colon; diet; docosahexaenoic acid; fructose; gas chromatography; genetic engineering; glutamic acid; herbal medicines; histopathology; inflammation; lipid metabolism; liquid chromatography; longevity; mass spectrometry; metabolites; metabolomics; mice; neoplasms; oxidation; proteome; tryptophan
Abstract:: ... American ginseng (Panax quinquefolius L.) is one of the most commonly used herbal medicines in the West. It has been reported to possess significant antitumor effects that inhibit the process of carcinogenesis. However, the mechanisms underlying its anticancer effects remain largely unresolved. In this study, we investigated the cancer chemopreventive effects of American ginseng on the progression ...
DOI:: 10.1021/acs.jproteome.5b00388
PubMed:: 26136108
PubMed Central:: PMC6098237
: https://doi.org/10.1021/acs.jproteome.5b00388

62. Network Marker Selection for Untargeted LC–MS Metabolomics Data

Author:: Cai Qingpo; Alvarez Jessica A.; Kang Jian; Yu Tianwei
Source:: Journal of Proteome Research 2017 v.16 no.3 pp. 1261-1269
ISSN:: 1535-3907
Subject:: biochemical pathways; body mass index; computer software; liquid chromatography; mass spectrometry; metabolites; metabolomics; proteome; screening; uncertainty
Abstract:: ... Untargeted metabolomics using high-resolution liquid chromatography–mass spectrometry (LC–MS) is becoming one of the major areas of high-throughput biology. Functional analysis, that is, analyzing the data based on metabolic pathways or the genome-scale metabolic network, is critical in feature selection and interpretation of metabolomics data. One of the main challenges in the functional analyses ...
DOI:: 10.1021/acs.jproteome.6b00861
PubMed:: 28168878
PubMed Central:: PMC5441461
: https://doi.org/10.1021/acs.jproteome.6b00861

63. Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements

Author:: Qian Chen; Hettich Robert L.
Source:: Journal of Proteome Research 2017 v.16 no.7 pp. 2537-2546
ISSN:: 1535-3907
Subject:: biogeochemical cycles; humic acids; ionization; liquid chromatography; mass spectrometry; microbial biomass; microbiome; pH; peptides; proteolysis; proteome; soil; soil sampling; solubility; trichloroacetic acid precipitation
Abstract:: ... The microbial composition and their activities in soil environments play a critical role in organic matter transformation and nutrient cycling. Liquid chromatography coupled to high-performance mass spectrometry provides a powerful approach to characterize soil microbiomes; however, the limited microbial biomass and the presence of abundant interferences in soil samples present major challenges to ...
DOI:: 10.1021/acs.jproteome.7b00103
: https://doi.org/10.1021/acs.jproteome.7b00103

64. Optimizing High-Resolution Mass Spectrometry for the Identification of Low-Abundance Post-Translational Modifications of Intact Proteins

Author:: Kilpatrick Lisa E.; Kilpatrick Eric L.
Source:: Journal of Proteome Research 2017 v.16 no.9 pp. 3255-3265
ISSN:: 1535-3907
Subject:: C-reactive protein; electric power; immunoglobulin G; liquid chromatography; mass spectrometry; monitoring; post-translational modification; proteome; spectrometers; temperature; transferrin; vitamin D-binding protein
Abstract:: ... Intact protein analysis by liquid chromatography–mass spectrometry (LC-MS) is now possible due to the improved capabilities of mass spectrometers yielding greater resolution, mass accuracy, and extended mass ranges. Concurrent measurement of post-translational modifications (PTMs) during LC-MS of intact proteins is advantageous while monitoring critical proteoform status, such as for clinical samp ...
DOI:: 10.1021/acs.jproteome.7b00244
: https://doi.org/10.1021/acs.jproteome.7b00244

65. Plasma Metabolite Biomarkers for the Detection of Pancreatic Cancer

Author:: Xie Guoxiang; Lu Lingeng; Qiu Yunping; Ni Quanxing; Zhang Wei; Gao Yu-Tang; Risch Harvey A.; Yu Herbert; Jia Wei
Source:: Journal of Proteome Research 2015 v.14 no.2 pp. 1195-1202
ISSN:: 1535-3907
Subject:: betaine; biomarkers; choline; confidence interval; data collection; graphs; liquid chromatography; mass spectrometry; metabolites; metabolomics; models; pancreatic neoplasms; patients; China; Connecticut
Abstract:: ... Patients with pancreatic cancer (PC) are usually diagnosed at late stages, when the disease is nearly incurable. Sensitive and specific markers are critical for supporting diagnostic and therapeutic strategies. The aim of this study was to use a metabonomics approach to identify potential plasma biomarkers that can be further developed for early detection of PC. In this study, plasma metabolites o ...
DOI:: 10.1021/pr501135f
PubMed:: 25429707
PubMed Central:: PMC4324440
: https://doi.org/10.1021/pr501135f

66. Profiling of Acylcarnitines in First Episode Psychosis before and after Antipsychotic Treatment

Author:: Kriisa Kärt; Leppik Liisa; Balõtšev Roman; Ottas Aigar; Soomets Ursel; Koido Kati; Volke Vallo; Innos Jürgen; Haring Liina; Vasar Eero; Zilmer Mihkel
Source:: Journal of Proteome Research 2017 v.16 no.10 pp. 3558-3566
ISSN:: 1535-3907
Subject:: antipsychotics; biomarkers; blood serum; body mass index; c-peptide; drug therapy; epidermal growth factor; flow injection analysis; insulin resistance; interleukin-2; interleukin-4; interleukin-6; leptin; linear models; liquid chromatography; metabolites; monitoring; patients; proteome; signal transduction; tandem mass spectrometry; transferases
Abstract:: ... Acylcarnitines (ACs) have been shown to have a potential to activate pro-inflammatory signaling pathways and to foster the development of insulin resistance. The first task of the current study was to study the full list of ACs (from C2 to C18) in first episode psychosis (FEP) patients before and after antipsychotic treatment. The second task was to relate ACs to inflammatory and metabolic biomark ...
DOI:: 10.1021/acs.jproteome.7b00279
: https://doi.org/10.1021/acs.jproteome.7b00279

67. Protein Quantification Using a Cleavable Reporter Peptide

Author:: Duriez Elodie; Trevisiol Stephane; Domon Bruno
Source:: Journal of Proteome Research 2015 v.14 no.2 pp. 728-737
ISSN:: 1535-3907
Subject:: biomarkers; cost effectiveness; isotope dilution technique; liquid chromatography; mass spectrometry; polypeptides; proteins; proteome; stable isotopes; urine
Abstract:: ... Peptide and protein quantification based on isotope dilution and mass spectrometry analysis are widely employed for the measurement of biomarkers and in system biology applications. The accuracy and reliability of such quantitative assays depend on the quality of the stable-isotope labeled standards. Although the quantification using stable-isotope labeled peptides is precise, the accuracy of the ...
DOI:: 10.1021/pr500764e
: https://doi.org/10.1021/pr500764e

68. Proteomics Analysis of EV71-Infected Cells Reveals the Involvement of Host Protein NEDD4L in EV71 Replication

Author:: Kuo Rei-Lin; Lin Ya-Han; Wang Robert Yung-Liang; Hsu Chia-Wei; Chiu Yi-Ting; Huang Hsing-I; Kao Li-Ting; Yu Jau-Song; Shih Shin-Ru; Wu Chih-Ching
Source:: Journal of Proteome Research 2015 v.14 no.4 pp. 1818-1830
ISSN:: 1535-3907
Subject:: Enterovirus A; children; gene expression regulation; hand, foot and mouth disease; humans; liquid chromatography; mass spectrometry; protein degradation; proteins; proteome; proteomics; viruses
Abstract:: ... Enterovirus 71 (EV71) is a human enterovirus that has seriously affected the Asia-Pacific area for the past two decades. EV71 infection can result in mild hand-foot-and-mouth disease and herpangina and may occasionally lead to severe neurological complications in children. However, the specific biological processes that become altered during EV71 infection remain unclear. To further explore host r ...
DOI:: 10.1021/pr501199h
: https://doi.org/10.1021/pr501199h

69. Proteomics Provides Insight into the Interaction between Mulberry and Silkworm

Author:: Wang Dandan; Dong Zhaoming; Zhang Yan; Guo Kaiyu; Guo Pengchao; Zhao Ping; Xia Qingyou
Source:: Journal of Proteome Research 2017 v.16 no.7 pp. 2472-2480
ISSN:: 1535-3907
Subject:: Bombyx mori; amino acids; chloroplasts; enzyme inhibition; feces; host plants; instars; jasmonic acid; larvae; leaves; liquid chromatography; metabolites; mitochondria; mulberries; phytophagous insects; proteinases; proteins; proteome; proteomics; silkworms; tandem mass spectrometry
Abstract:: ... Mulberry leaves have been selected as a food source for the silkworm (Bombyx mori) for over 5000 years. However, the interaction mechanisms of mulberry–silkworm remain largely unknown. We explore the interaction between mulberry and silkworm at the protein level. Total proteins were extracted from mulberry leaves and silkworm feces on day 5 of the fifth larval instar and analyzed on shotgun liquid ...
DOI:: 10.1021/acs.jproteome.7b00071
: https://doi.org/10.1021/acs.jproteome.7b00071

70. Qualitative and Quantitative Analysis of Proteome and Peptidome of Human Follicular Fluid Using Multiple Samples from Single Donor with LC–MS and SWATH Methodology

Author:: Lewandowska Aleksandra E.; Macur Katarzyna; Czaplewska Paulina; Liss Joanna; Łukaszuk Krzysztof; Ołdziej Stanisław
Source:: Journal of Proteome Research 2017 v.16 no.8 pp. 3053-3067
ISSN:: 1535-3907
Subject:: biomarkers; follicular fluid; humans; liquid chromatography; mass spectrometry; oocytes; peptides; proteins; proteome; quantitative analysis; ultrafiltration
Abstract:: ... Human follicular fluid (hFF) is a natural environment of oocyte maturation, and some components of hFF could be used to judge oocyte capability for fertilization and further development. In our pilot small-scale study three samples from four donors (12 samples in total) were analyzed to determine which hFF proteins/peptides could be used to differentiate individual oocytes and which are patient-sp ...
DOI:: 10.1021/acs.jproteome.7b00366
: https://doi.org/10.1021/acs.jproteome.7b00366

71. Quantification of Total Vitamin-D-Binding Protein and the Glycosylated Isoforms by Liquid Chromatography–Isotope Dilution Mass Spectrometry

Author:: Kilpatrick Lisa E.; Phinney Karen W.
Source:: Journal of Proteome Research 2017 v.16 no.11 pp. 4185-4195
ISSN:: 1535-3907
Subject:: amino acids; digestion; glycosylation; guanidines; isotope dilution technique; liquid chromatography; liquids; mass spectrometry; metabolites; peptides; protein content; protein sources; proteome; urea
Abstract:: ... Vitamin-D-binding protein (VDBP), a transporter of 25-hydroxyvitamin D metabolites, has three common isoforms. The relationship of the isoforms and their glycosylation state with various diseases has been under recent examination. In this work, liquid chromatography coupled to isotope dilution mass spectrometry was evaluated for quantification of VDBP, the three common isoforms, and total glycosyl ...
DOI:: 10.1021/acs.jproteome.7b00560
: https://doi.org/10.1021/acs.jproteome.7b00560

72. Quantitative Label-Free Phosphoproteomics Reveals Differentially Regulated Protein Phosphorylation Involved in West Nile Virus-Induced Host Inflammatory Response

Author:: Zhang Hao; Sun Jun; Ye Jing; Ashraf Usama; Chen Zheng; Zhu Bibo; He Wen; Xu Qiuping; Wei Yanming; Chen Huanchun; Fu Zhen F.; Liu Rong; Cao Shengbo
Source:: Journal of Proteome Research 2015 v.14 no.12 pp. 5157-5168
ISSN:: 1535-3907
Subject:: West Nile virus; central nervous system; cytokines; gene ontology; glycogen (starch) synthase; humans; immunopathology; inflammation; liquid chromatography; phosphoproteins; protein phosphorylation; proteome; proteomics; spliceosomes; tandem mass spectrometry; target of rapamycin signaling pathways; transcription factor NF-kappa B; viruses
Abstract:: ... West Nile virus (WNV) can cause neuro-invasive and febrile illness that may be fatal to humans. The production of inflammatory cytokines is key to mediating WNV-induced immunopathology in the central nervous system. Elucidating the host factors utilized by WNV for productive infection would provide valuable insights into the evasion strategies used by this virus. Although attempts have been made t ...
DOI:: 10.1021/acs.jproteome.5b00424
: https://doi.org/10.1021/acs.jproteome.5b00424

73. Rapid Characterization of the Human Breast Milk Lipidome Using a Solid-Phase Microextraction and Liquid Chromatography–Mass Spectrometry-Based Approach

Author:: Garwolińska Dorota; Hewelt-Belka Weronika; Namieśnik Jacek; Kot-Wasik Agata
Source:: Journal of Proteome Research 2017 v.16 no.9 pp. 3200-3208
ISSN:: 1535-3907
Subject:: bioactive compounds; breast feeding; breast milk; carbohydrates; chloroform; databases; infants; lipid composition; lipids; liquid chromatography; liquids; mass spectrometry; milk composition; minerals; nutrient content; proteins; proteome; qualitative analysis; solid phase microextraction; solvents; toxicity
Abstract:: ... Human breast milk (HBM) is a biofluid consisting of various biomolecules such as proteins, lipids, carbohydrates, minerals and bioactive substances. Due to its unique and complex composition, HBM provides not only nutritional components required for the growth of the infant, but also additional protection against infections. Global insight into the composition of HBM is crucial to understanding th ...
DOI:: 10.1021/acs.jproteome.7b00195
: https://doi.org/10.1021/acs.jproteome.7b00195

74. Shotgun Ecotoxicoproteomics of Daphnia pulex: Biochemical Effects of the Anticancer Drug Tamoxifen

Author:: Borgatta Myriam; Hernandez Céline; Decosterd Laurent Arthur; Chèvre Nathalie; Waridel Patrice
Source:: Journal of Proteome Research 2015 v.14 no.1 pp. 279-291
ISSN:: 1535-3907
Subject:: Daphnia pulex; carbohydrates; data collection; environmental impact; lipid metabolism; liquid chromatography; mass spectrometry; pollutants; protein degradation; protein synthesis; proteins; proteome; proteomics; reproduction; stress response; tamoxifen; xenobiotics
Abstract:: ... Among pollutants released into the environment by human activities, residues of pharmaceuticals are an increasing matter of concern because of their potential impact on ecosystems. The aim of this study was to analyze differences of protein expression resulting from acute (2 days) and middle-term (7 days) exposure of aquatic microcrustacean Daphnia pulex to the anticancer drug tamoxifen. Using a l ...
DOI:: 10.1021/pr500916m
: https://doi.org/10.1021/pr500916m

75. Site-Specific Glycosylation of Secretory Immunoglobulin A from Human Colostrum

Author:: Huang Jincui; Guerrero Andres; Parker Evan; Strum John S.; Smilowitz Jennifer T.; German J. Bruce; Lebrilla Carlito B.
Source:: Journal of Proteome Research 2015 v.14 no.3 pp. 1335-1349
ISSN:: 1535-3907
Subject:: computer software; digestive tract mucosa; glycopeptides; glycoproteins; glycosylation; human colostrum; immunoglobulin A; liquid chromatography; mass spectrometry; milk; polysaccharides; proteinases; proteome
Abstract:: ... Secretory immunoglobulin A (sIgA) is a major glycoprotein in milk and plays a key role in mediating immune protection of the gut mucosa. Although it is a highly glycosylated protein, its site-specific glycosylation and associated glycan micro-heterogeneity have still not been fully elucidated. In this study, the site-specific glycosylation of sIgA isolated from human colostrum (n = 3) was analyzed ...
DOI:: 10.1021/pr500826q
PubMed:: 25629924
PubMed Central:: PMC5519350
: https://doi.org/10.1021/pr500826q

76. Systematic Optimization of Long Gradient Chromatography Mass Spectrometry for Deep Analysis of Brain Proteome

Author:: Wang Hong; Yang Yanling; Li Yuxin; Bai Bing; Wang Xusheng; Tan Haiyan; Liu Tao; Beach Thomas G.; Peng Junmin; Wu Zhiping
Source:: Journal of Proteome Research 2015 v.14 no.2 pp. 829-838
ISSN:: 1535-3907
Subject:: Alzheimer disease; acetonitrile; brain; fractionation; gases; gene expression; ions; liquid chromatography; mass spectrometry; pH; peptides; protein content; proteins; proteome; proteomics; sequence analysis
Abstract:: ... The development of high-resolution liquid chromatography (LC) is essential for improving the sensitivity and throughput of mass spectrometry (MS)-based proteomics. Here we present systematic optimization of a long gradient LC–MS/MS platform to enhance protein identification from a complex mixture. The platform employed an in-house fabricated, reverse-phase long column (100 μm × 150 cm, 5 μm C18 be ...
DOI:: 10.1021/pr500882h
PubMed:: 25455107
PubMed Central:: PMC4324436
: https://doi.org/10.1021/pr500882h

77. Targeted Proteomic Analyses of Nasal Lavage Fluid in Persulfate-Challenged Hairdressers with Bleaching Powder-Associated Rhinitis

Author:: Mörtstedt Harriet; Ali Neserin; Kåredal Monica; Jacobsson Helene; Rietz Emelie; Kronholm Diab Kerstin; Nielsen Jörn; Jönsson Bo A.G.; Lindh Christian H.
Source:: Journal of Proteome Research 2015 v.14 no.2 pp. 860-873
ISSN:: 1535-3907
Subject:: albumins; asthma; biomarkers; bleaching; epithelium; inflammation; liquid chromatography; monitoring; nose; oxidants; oxidation; oxidative stress; pathogenesis; peptides; proteome; proteomics; rhinitis; risk; tandem mass spectrometry; tryptophan
Abstract:: ... Hairdressers have an increased risk for developing airway symptoms, for example, asthma and rhinitis. Persulfates, which are oxidizing agents in bleaching powder, are considered important causal agents for these symptoms. However, the underlying mechanisms are unclear. The aim was therefore to measure proteomic changes in nasal lavage fluid from persulfate-challenged subjects to identify proteins ...
DOI:: 10.1021/pr5009306
: https://doi.org/10.1021/pr5009306

78. Thermal Shock Induces Host Proteostasis Disruption and Endoplasmic Reticulum Stress in the Model Symbiotic Cnidarian Aiptasia

Author:: Oakley Clinton A.; Durand Elysanne; Wilkinson Shaun P.; Peng Lifeng; Weis Virginia M.; Grossman Arthur R.; Davy Simon K.
Source:: Journal of Proteome Research 2017 v.16 no.6 pp. 2121-2134
ISSN:: 1535-3907
Subject:: Cnidaria; acclimation; bleaching; coral bleaching; corals; ecological function; endoplasmic reticulum; endoplasmic reticulum stress; heat stress; homeostasis; liquid chromatography; models; photoinhibition; protein folding; protein synthesis; proteome; reactive oxygen species; structural proteins; symbionts; tandem mass spectrometry; temperature
Abstract:: ... Coral bleaching has devastating effects on coral survival and reef ecosystem function, but many of the fundamental cellular effects of thermal stress on cnidarian physiology are unclear. We used label-free liquid chromatography–tandem mass spectrometry to compare the effects of rapidly (33.5 °C, 24 h) and gradually (30 and 33.5 °C, 12 days) elevated temperatures on the proteome of the model symbio ...
DOI:: 10.1021/acs.jproteome.6b00797
: https://doi.org/10.1021/acs.jproteome.6b00797

79. Third-Generation Electrokinetically Pumped Sheath-Flow Nanospray Interface with Improved Stability and Sensitivity for Automated Capillary Zone Electrophoresis–Mass Spectrometry Analysis of Complex Proteome Digests

Author:: Sun Liangliang; Zhu Guijie; Zhang Zhenbin; Mou Si; Dovichi Norman J.
Source:: Journal of Proteome Research 2015 v.14 no.5 pp. 2312-2321
ISSN:: 1535-3907
Subject:: Xenopus laevis; bovine serum albumin; capillary zone electrophoresis; data collection; eggs; liquid chromatography; mass spectrometry; peptides; proteome; proteomics; spectrometers; statistical analysis
Abstract:: ... We have reported a set of electrokinetically pumped sheath flow nanoelectrospray interfaces to couple capillary zone electrophoresis with mass spectrometry. A separation capillary is threaded through a cross into a glass emitter. A side arm provides fluidic contact with a sheath buffer reservoir that is connected to a power supply. The potential applied to the sheath buffer drives electro-osmosis ...
DOI:: 10.1021/acs.jproteome.5b00100
PubMed:: 25786131
PubMed Central:: PMC4416984
: https://doi.org/10.1021/acs.jproteome.5b00100

80. Whole Grain Consumption Increases Gastrointestinal Content of Sulfate-Conjugated Oxylipins in Pigs − A Multicompartmental Metabolomics Study

Author:: Ingerslev Anne Krog; Karaman Ibrahim; Bağcıoğlu Murat; Kohler Achim; Theil Peter Kappel; Bach Knudsen Knud Erik; Hedemann Mette Skou
Source:: Journal of Proteome Research 2015 v.14 no.8 pp. 3095-3110
ISSN:: 1535-3907
Subject:: Western diets; bioavailability; biomarkers; dietary fiber; fermented foods; gastrointestinal system; grain consumption; liquid chromatography; mass spectrometry; metabolites; metabolomics; multivariate analysis; nutrients; nutritional intervention; oxylipins; phenolic compounds; proteome; resistant starch; rye; secretion; sulfates; swine; urine; wheat bran; whole grain foods
Abstract:: ... The effects of increased intake of dietary fiber as either whole grain rye or as resistant starch compared to a typical low dietary fiber Western-style diet on the metabolomics responses were studied in gastrointestinal content and tissue, peripheral plasma, and urine using a multicompartmental nontargeted liquid chromatography–mass spectrometry (LC–MS) approach in pigs. Both unsupervised and supe ...
DOI:: 10.1021/acs.jproteome.5b00039
: https://doi.org/10.1021/acs.jproteome.5b00039

81. 193 nm Ultraviolet Photodissociation Mass Spectrometry for Phosphopeptide Characterization in the Positive and Negative Ion Modes

Author:: Robinson Michelle R.; Taliaferro Juliana M.; Dalby Kevin N.; Brodbelt Jennifer S.
Source:: Journal of Proteome Research 2016 v.15 no.8 pp. 2739-2748
ISSN:: 1535-3907
Subject:: casein; data collection; dissociation; energy; ionization; ions; liquid chromatography; phosphates; phosphopeptides; photolysis; proteome; proteomics; tandem mass spectrometry
Abstract:: ... Advances in liquid chromatography tandem mass spectrometry (LC–MS/MS) have permitted phosphoproteomic analysis on a grand scale, but ongoing challenges specifically associated with confident phosphate localization continue to motivate the development of new fragmentation techniques. In the present study, ultraviolet photodissociation (UVPD) at 193 nm is evaluated for the characterization of phosph ...
DOI:: 10.1021/acs.jproteome.6b00289
PubMed:: 27425180
PubMed Central:: PMC5481846
: https://doi.org/10.1021/acs.jproteome.6b00289

82. A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline

Author:: Rudnick Paul A.; Markey Sanford P.; Roth Jeri; Mirokhin Yuri; Yan Xinjian; Tchekhovskoi Dmitrii V.; Edwards Nathan J.; Thangudu Ratna R.; Ketchum Karen A.; Kinsinger Christopher R.; Mesri Mehdi; Rodriguez Henry; Stein Stephen E.
Source:: Journal of Proteome Research 2016 v.15 no.3 pp. 1023-1032
ISSN:: 1535-3907
Subject:: breasts; colon; computer software; data collection; databases; genome; genomics; liquid chromatography; neoplasms; phosphopeptides; proteome; proteomics; tandem mass spectrometry; tissues
Abstract:: ... The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has produced large proteomics data sets from the mass spectrometric interrogation of tumor samples previously analyzed by The Cancer Genome Atlas (TCGA) program. The availability of the genomic and proteomic data is enabling proteogenomic study for both reference (i.e., contained in major sequence databases) and nonreference markers of cance ...
DOI:: 10.1021/acs.jproteome.5b01091
PubMed:: 26860878
PubMed Central:: PMC5117628
: https://doi.org/10.1021/acs.jproteome.5b01091

83. A Proteomics Strategy for the Identification of FAT10-Modified Sites by Mass Spectrometry

Author:: Leng Ling; Xu Changming; Wei Chao; Zhang Jiyang; Liu Boya; Ma Jie; Li Ning; Qin Weijie; Zhang Wanjun; Zhang Chengpu; Xing Xiaohua; Zhai Linhui; Yang Fan; Li Mansheng; Jin Chaozhi; Yuan Yanzhi; Xu Ping; Qin Jun; Xie Hongwei; He Fuchu; Wang Jian
Source:: Journal of Proteome Research 2014 v.13 no.1 pp. 268-276
ISSN:: 1535-3907
Subject:: RNA; amino acids; apoptosis; chemical bonding; eukaryotic cells; humans; hydrophilicity; immune response; liquid chromatography; loci; major histocompatibility complex; neoplasms; precipitin tests; proliferating cell nuclear antigen; protein folding; proteome; proteomics; tandem mass spectrometry
Abstract:: ... The ubiquitin-like protein FAT10 (HLA-F adjacent transcript 10) is uniquely expressed in mammals. The fat10 gene is encoded in the MHC class I locus in the human genome and is related to some specific processes, such as apoptosis, immune response, and cancer. However, biological knowledge of FAT10 is limited, owing to the lack of identification of its conjugates. FAT10 covalently modifies proteins ...
DOI:: 10.1021/pr400395k
: https://doi.org/10.1021/pr400395k

84. Adaptation of Skyline for Targeted Lipidomics

Author:: Peng Bing; Ahrends Robert
Source:: Journal of Proteome Research 2016 v.15 no.1 pp. 291-301
ISSN:: 1535-3907
Subject:: bioinformatics; cholesterol; cholesteryl esters; computer software; energy; fatty acids; mass spectrometry; monitoring; proteome; proteomics; screening; sphingolipids; stem cells
Abstract:: ... In response to the urgent need for analysis software that is capable of handling data from targeted high-throughput lipidomics experiments, we here present a systematic workflow for the straightforward method design and analysis of selected reaction monitoring data in lipidomics based on lipid building blocks. Skyline is a powerful software primarily designed for proteomics applications where it i ...
DOI:: 10.1021/acs.jproteome.5b00841
: https://doi.org/10.1021/acs.jproteome.5b00841

85. Advanced Precursor Ion Selection Algorithms for Increased Depth of Bottom-Up Proteomic Profiling

Author:: Kreimer Simion; Belov Mikhail E.; Danielson William F.; Levitsky Lev I.; Gorshkov Mikhail V.; Karger Barry L.; Ivanov Alexander R.
Source:: Journal of Proteome Research 2016 v.15 no.10 pp. 3563-3573
ISSN:: 1535-3907
Subject:: algorithms; human cell lines; liquid chromatography; mass spectrometry; peptides; proteome; proteomics; spectrometers
Abstract:: ... Conventional TopN data-dependent acquisition (DDA) LC–MS/MS analysis identifies only a limited fraction of all detectable precursors because the ion-sampling rate of contemporary mass spectrometers is insufficient to target each precursor in a complex sample. TopN DDA preferentially targets high-abundance precursors with limited sampling of low-abundance precursors and repeated analyses only margi ...
DOI:: 10.1021/acs.jproteome.6b00312
PubMed:: 27569903
PubMed Central:: PMC5557716
: https://doi.org/10.1021/acs.jproteome.6b00312

86. An Automated Pipeline to Monitor System Performance in Liquid Chromatography–Tandem Mass Spectrometry Proteomic Experiments

Author:: Bereman Michael S.; Beri Joshua; Sharma Vagisha; Nathe Cory; Eckels Josh; MacLean Brendan; MacCoss Michael J.
Source:: Journal of Proteome Research 2016 v.15 no.12 pp. 4763-4769
ISSN:: 1535-3907
Subject:: Internet; computers; data collection; liquid chromatography; monitoring; peptides; process control; proteome; proteomics; tandem mass spectrometry
Abstract:: ... We report the development of a completely automated pipeline to monitor system suitability in bottom-up proteomic experiments. LC–MS/MS runs are automatically imported into Skyline and multiple identification-free metrics are extracted from targeted peptides. These data are then uploaded to the Panorama Skyline document repository where metrics can be viewed in a web-based interface using powerful ...
DOI:: 10.1021/acs.jproteome.6b00744
PubMed:: 27700092
PubMed Central:: PMC5406750
: https://doi.org/10.1021/acs.jproteome.6b00744

87. Assignment of Saccharide Identities through Analysis of Oxonium Ion Fragmentation Profiles in LC–MS/MS of Glycopeptides

Author:: Halim Adnan; Westerlind Ulrika; Pett Christian; Schorlemer Manuel; Rüetschi Ulla; Brinkmalm Gunnar; Sihlbom Carina; Lengqvist Johan; Larson Göran; Nilsson Jonas
Source:: Journal of Proteome Research 2014 v.13 no.12 pp. 6024-6032
ISSN:: 1535-3907
Subject:: biochemical pathways; constitutional isomers; dissociation; glycopeptides; glycosylation; ions; liquid chromatography; proteome; structure-activity relationships; tandem mass spectrometry
Abstract:: ... Protein glycosylation plays critical roles in the regulation of diverse biological processes, and determination of glycan structure–function relationships is important to better understand these events. However, characterization of glycan and glycopeptide structural isomers remains challenging and often relies on biosynthetic pathways being conserved. In glycoproteomic analysis with liquid chromat ...
DOI:: 10.1021/pr500898r
: https://doi.org/10.1021/pr500898r

88. Automated SDS Depletion for Mass Spectrometry of Intact Membrane Proteins though Transmembrane Electrophoresis

Author:: Kachuk Carolyn; Faulkner Melissa; Liu Fang; Doucette Alan A.
Source:: Journal of Proteome Research 2016 v.15 no.8 pp. 2634-2642
ISSN:: 1535-3907
Subject:: Escherichia coli; electric current; electrophoresis; electrospray ionization mass spectrometry; hydrophobicity; liquid chromatography; membrane proteins; microfiltration; proteome; proteomics; sodium dodecyl sulfate; solubility; surfactants
Abstract:: ... Membrane proteins are underrepresented in proteome analysis platforms because of their hydrophobic character, contributing to decreased solubility. Sodium dodecyl sulfate is a favored denaturant in proteomic workflows, facilitating cell lysis and protein dissolution; however, SDS impedes MS detection and therefore must be removed prior to analysis. Although strategies exist for SDS removal, they p ...
DOI:: 10.1021/acs.jproteome.6b00199
: https://doi.org/10.1021/acs.jproteome.6b00199

89. Cd2+-Induced Alteration of the Global Proteome of Human Skin Fibroblast Cells

Author:: Prins John M.; Fu Lijuan; Guo Lei; Wang Yinsheng
Source:: Journal of Proteome Research 2014 v.13 no.3 pp. 1677-1687
ISSN:: 1535-3907
Subject:: amino acids; antioxidants; biosynthesis; cadmium; carcinogens; cell culture; energy metabolism; fibroblasts; glutathione; glutathione peroxidase; glutathione synthase; glutathione transferase; glycolysis; heavy metals; homeostasis; humans; isotope labeling; liquid chromatography; lungs; mechanism of action; nitric oxide; pentose phosphate cycle; proteins; proteome; proteomics; skin (animal); stable isotopes; superoxide dismutase; tandem mass spectrometry; toxicity; tricarboxylic acid cycle
Abstract:: ... Cadmium (Cd²⁺) is a toxic heavy metal and a well-known human carcinogen. The toxic effects of Cd²⁺ on biological systems are diverse and thought to be exerted through a complex array of mechanisms. Despite the large number of studies aimed to elucidate the toxic mechanisms of action of Cd²⁺, few have been targeted toward investigating the ability of Cd²⁺ to disrupt multiple cellular pathways simul ...
DOI:: 10.1021/pr401159f
PubMed:: 24527689
PubMed Central:: PMC3993958
: https://doi.org/10.1021/pr401159f

90. Cinnamaldehyde Characterization as an Antibacterial Agent toward E. coli Metabolic Profile Using 96-Blade Solid-Phase Microextraction Coupled to Liquid Chromatography–Mass Spectrometry

Author:: Mousavi Fatemeh; Bojko Barbara; Bessonneau Vincent; Pawliszyn Janusz
Source:: Journal of Proteome Research 2016 v.15 no.3 pp. 963-975
ISSN:: 1535-3907
Subject:: Escherichia coli; antibiotics; bacteria; biochemical pathways; carbohydrates; drugs; food safety; lipids; liquid chromatography; mass spectrometry; metabolism; metabolites; metabolome; microbial culture; nucleic acids; oxidative stress; proteins; proteome; proteomics; solid phase microextraction; transcriptomics
Abstract:: ... Sampling and sample preparation plays an important role in untargeted analysis as it influences final composition of the analyzed extract and consequently reflection of the metabolome. In the current work, mechanism of bactericidal action of cinnamaldehyde (CA) against Escherichia coli (E. coli) during bacteria growth applying high-throughput solid-phase microextraction in direct immersion mode co ...
DOI:: 10.1021/acs.jproteome.5b00992
: https://doi.org/10.1021/acs.jproteome.5b00992

91. Combination of Bottom-up 2D-LC-MS and Semi-top-down GelFree-LC-MS Enhances Coverage of Proteome and Low Molecular Weight Short Open Reading Frame Encoded Peptides of the Archaeon Methanosarcina mazei

Author:: Cassidy Liam; Prasse Daniela; Linke Dennis; Schmitz Ruth A.; Tholey Andreas
Source:: Journal of Proteome Research 2016 v.15 no.10 pp. 3773-3783
ISSN:: 1535-3907
Subject:: Methanosarcina mazei; databases; digestion; genes; liquid chromatography; mass spectrometry; methane; molecular weight; open reading frames; pH; peptides; proteins; proteome
Abstract:: ... The recent discovery of an increasing number of small open reading frames (sORF) creates the need for suitable analytical technologies for the comprehensive identification of the corresponding gene products. For biological and functional studies the knowledge of the entire set of proteins and sORF gene products is essential. Consequently in the present study we evaluated analytical approaches that ...
DOI:: 10.1021/acs.jproteome.6b00569
: https://doi.org/10.1021/acs.jproteome.6b00569

92. Comparative Analysis of the Endogenous Peptidomes Displayed by HLA-B27 and Mamu-B08: Two MHC Class I Alleles Associated with Elite Control of HIV/SIV Infection

Author:: Marcilla Miguel; Alvarez Iñaki; Ramos-Fernández Antonio; Lombardía Manuel; Paradela Alberto; Albar Juan Pablo
Source:: Journal of Proteome Research 2016 v.15 no.3 pp. 1059-1069
ISSN:: 1535-3907
Subject:: HIV infections; Human immunodeficiency virus; Macaca mulatta; alleles; animal models; arginine; binding capacity; epitopes; glutamine; humans; leucine; ligands; liquid chromatography; major histocompatibility complex; mass spectrometry; molecular weight; peptides; phenylalanine; proteome; sequence homology; tyrosine
Abstract:: ... Indian rhesus macaques are arguably the most reliable animal models in AIDS research. In this species the MHC class I allele Mamu-B*08, among others, is associated with elite control of SIV replication. A similar scenario is observed in humans where the expression of HLA-B*27 or HLA-B*57 has been linked to slow or no progression to AIDS after HIV infection. Despite having large differences in thei ...
DOI:: 10.1021/acs.jproteome.5b01146
: https://doi.org/10.1021/acs.jproteome.5b01146

93. Comparative Studies of the Proteome, Glycoproteome, and N-Glycome of Clear Cell Renal Cell Carcinoma Plasma before and after Curative Nephrectomy

Author:: Gbormittah Francisca O.; Lee Ling Y.; Taylor KyOnese; Hancock William S.; Iliopoulos Othon
Source:: Journal of Proteome Research 2014 v.13 no.11 pp. 4889-4900
ISSN:: 1535-3907
Subject:: biomarkers; early diagnosis; fractionation; gene expression regulation; glycoproteins; glycoproteomics; glycosylation; liquid chromatography; patients; prognosis; proteome; qualitative analysis; relapse; renal cell carcinoma; survival rate; tandem mass spectrometry
Abstract:: ... Clear cell renal cell carcinoma is the most prevalent of all reported kidney cancer cases, and currently there are no markers for early diagnosis. This has stimulated great research interest recently because early detection of the disease can significantly improve the low survival rate. Combining the proteome, glycoproteome, and N-glycome data from clear cell renal cell carcinoma plasma has the po ...
DOI:: 10.1021/pr500591e
PubMed:: 25184692
PubMed Central:: PMC4227548
: https://doi.org/10.1021/pr500591e

94. Efficient Microscale Basic Reverse Phase Peptide Fractionation for Global and Targeted Proteomics

Author:: Lee Hyoung-Joo; Kim Hye-Jung; Liebler Daniel C.
Source:: Journal of Proteome Research 2016 v.15 no.7 pp. 2346-2354
ISSN:: 1535-3907
Subject:: cell lines; enzyme inhibitors; fractionation; gene expression regulation; inventories; liquid chromatography; lung neoplasms; monitoring; neoplasm cells; protein synthesis; proteins; proteome; proteomics; receptor protein-tyrosine kinase; tyrosine
Abstract:: ... Analysis of small biological samples would benefit from an efficient microscale fractionation strategy that minimizes sample handling, transfer steps, and accompanying losses. Here we describe a microscale basic reverse phase liquid chromatographic (bRPLC) fractionation method that offers high reproducibility and efficiency for peptide mixtures from small (5–20 μg) samples. We applied our platform ...
DOI:: 10.1021/acs.jproteome.6b00102
PubMed:: 27255222
PubMed Central:: PMC5785084
: https://doi.org/10.1021/acs.jproteome.6b00102

95. Elucidating Proteoform Families from Proteoform Intact-Mass and Lysine-Count Measurements

Author:: Shortreed Michael R.; Frey Brian L.; Scalf Mark; Knoener Rachel A.; Cesnik Anthony J.; Smith Lloyd M.
Source:: Journal of Proteome Research 2016 v.15 no.4 pp. 1213-1221
ISSN:: 1535-3907
Subject:: digestion; liquid chromatography; lysine; mass spectrometry; peptides; proteins; proteome; proteomics; spectrometers; yeasts
Abstract:: ... Proteomics is presently dominated by the “bottom-up” strategy, in which proteins are enzymatically digested into peptides for mass spectrometric identification. Although this approach is highly effective at identifying large numbers of proteins present in complex samples, the digestion into peptides renders it impossible to identify the proteoforms from which they were derived. We present here a p ...
DOI:: 10.1021/acs.jproteome.5b01090
PubMed:: 26941048
PubMed Central:: PMC4917391
: https://doi.org/10.1021/acs.jproteome.5b01090

96. Elucidating the “Gravome”: Quantitative Proteomic Profiling of the Response to Chronic Hypergravity in Drosophila

Author:: Hosamani Ravikumar; Leib Ryan; Bhardwaj Shilpa R.; Adams Christopher M.; Bhattacharya Sharmila
Source:: Journal of Proteome Research 2016 v.15 no.12 pp. 4165-4175
ISSN:: 1535-3907
Subject:: Drosophila melanogaster; adenosinetriphosphatase; adults; calcium; chitin; females; fruit flies; gene ontology; gravity; head; immune response; liquid chromatography; metabolism; proteins; proteome; proteomics; space flight; surveys; tandem mass spectrometry; transcriptomics
Abstract:: ... Altered gravity conditions, such as experienced by organisms during spaceflight, are known to cause transcriptomic and proteomic changes. We describe the proteomic changes in whole adult Drosophila melanogaster (fruit fly) but focus specifically on the localized changes in the adult head in response to chronic hypergravity (3 g) treatment. Canton S adult female flies (2 to 3 days old) were exposed ...
DOI:: 10.1021/acs.jproteome.6b00030
: https://doi.org/10.1021/acs.jproteome.6b00030

97. Exploring Potential Virulence Regulators in Paracoccidioides brasiliensis Isolates of Varying Virulence through Quantitative Proteomics

Author:: Castilho Daniele G.; Chaves Alison F. A.; Xander Patricia; Zelanis André; Kitano Eduardo S.; Serrano Solange M. T.; Tashima Alexandre K.; Batista Wagner L.
Source:: Journal of Proteome Research 2014 v.13 no.10 pp. 4259-4271
ISSN:: 1535-3907
Subject:: Paracoccidioides brasiliensis; gene expression regulation; genes; host-pathogen relationships; liquid chromatography; mice; pathogens; proteins; proteome; proteomics; tandem mass spectrometry; virulence; yeasts
Abstract:: ... Few virulence factors have been identified for Paracoccidioides brasiliensis, the agent of paracoccidioidomycosis. In this study, we quantitatively evaluated the protein composition of P. brasiliensis in the yeast phase using minimal and rich media to obtain a better understanding of its virulence and to gain new insights into pathogen adaptation strategies. This analysis was performed on two isol ...
DOI:: 10.1021/pr5002274
: https://doi.org/10.1021/pr5002274

98. Gaussian Process Modeling of Protein Turnover

Author:: Rahman Mahbubur; Previs Stephen F.; Kasumov Takhar; Sadygov Rovshan G.
Source:: Journal of Proteome Research 2016 v.15 no.7 pp. 2115-2122
ISSN:: 1535-3907
Subject:: brain; computer software; data collection; deuterium oxide; differential equation; heart failure; liquid chromatography; liver; mass spectrometry; mice; models; normal distribution; protein metabolism; proteins; proteome; rats; stable isotopes; stochastic processes; variance covariance matrix
Abstract:: ... We describe a stochastic model to compute in vivo protein turnover rate constants from stable-isotope labeling and high-throughput liquid chromatography–mass spectrometry experiments. We show that the often-used one- and two-compartment nonstochastic models allow explicit solutions from the corresponding stochastic differential equations. The resulting stochastic process is a Gaussian processes wi ...
DOI:: 10.1021/acs.jproteome.5b00990
PubMed:: 27229456
PubMed Central:: PMC5292319
: https://doi.org/10.1021/acs.jproteome.5b00990

99. Genetic Manipulation of Isoprene Emissions in Poplar Plants Remodels the Chloroplast Proteome

Author:: Velikova Violeta; Ghirardo Andrea; Vanzo Elisa; Merl Juliane; Hauck Stefanie M.; Schnitzler Jörg-Peter
Source:: Journal of Proteome Research 2014 v.13 no.4 pp. 2005-2018
ISSN:: 1535-3907
Subject:: Populus; RNA interference; abiotic stress; emissions; genetic engineering; histones; isoprene; liquid chromatography; photosynthesis; plant tissues; polyacrylamide gel electrophoresis; protein composition; proteome; reactive oxygen species; ribosomal proteins; tandem mass spectrometry; thylakoids
Abstract:: ... Biogenic isoprene (2-methyl-1,3-butadiene) improves the integrity and functionality of thylakoid membranes and scavenges reactive oxygen species (ROS) in plant tissue under stress conditions. On the basis of available physiological studies, we hypothesized that the suppression of isoprene production in the poplar plant by genetic engineering would cause changes in the chloroplast protein pattern, ...
DOI:: 10.1021/pr401124z
: https://doi.org/10.1021/pr401124z

100. Global Metabolomic and Isobaric Tagging Capillary Liquid Chromatography–Tandem Mass Spectrometry Approaches for Uncovering Pathway Dysfunction in Diabetic Mouse Aorta

Author:: Filla Laura A.; Yuan Wei; Feldman Eva L.; Li Shuwei; Edwards James L.
Source:: Journal of Proteome Research 2014 v.13 no.12 pp. 6121-6134
ISSN:: 1535-3907
Subject:: amines; amino acid metabolism; animal disease models; aorta; biochemical pathways; biomarkers; carbohydrate metabolism; diabetic complications; hyperglycemia; hyperlipidemia; hypertension; liquid chromatography; metabolites; metabolomics; mice; pathogenesis; proteome; risk; tandem mass spectrometry
Abstract:: ... Despite the prevalence of diabetes and the global health risks it poses, the biochemical pathogenesis of diabetic complications remains poorly understood with few effective therapies. This study employs capillary liquid chromatography (capLC) and tandem mass spectrometry (MS/MS) in conjunction with both global metabolomics and isobaric tags specific to amines and carbonyls to probe aortic metaboli ...
DOI:: 10.1021/pr501030e
PubMed:: 25368974
PubMed Central:: PMC4261973
: https://doi.org/10.1021/pr501030e

PubAg

Main content area

Limit your search

Text Availability

Journal

Publication Year

Subject

Search

340 Search Results

Search Results

1. Acid/Salt/pH Gradient Improved Resolution and Sensitivity in Proteomics Study Using 2D SCX-RP LC–MS

2. An IonStar Experimental Strategy for MS1 Ion Current-Based Quantification Using Ultrahigh-Field Orbitrap: Reproducible, In-Depth, and Accurate Protein Measurement in Large Cohorts

3. Brachyspira hyodysenteriae Infection Regulates Mucin Glycosylation Synthesis Inducing an Increased Expression of Core-2 O-Glycans in Porcine Colon

4. Discrimination of Four Marine Biofilm-Forming Bacteria by LC–MS Metabolomics and Influence of Culture Parameters

5. Effect of Antibiotics and Diet on Enterolactone Concentration and Metabolome Studied by Targeted and Nontargeted LC–MS Metabolomics

6. Elucidating Escherichia coli Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database

7. Feasibility of Early Detection of Cystic Fibrosis Acute Pulmonary Exacerbations by Exhaled Breath Condensate Metabolomics: A Pilot Study

8. Flagging False Positives Following Untargeted LC–MS Characterization of Histone Post-Translational Modification Combinations

9. Identification of Alternative Splice Variants Using Unique Tryptic Peptide Sequences for Database Searches

10. Improved Reversed Phase Chromatography of Hydrophilic Peptides from Spatial and Temporal Changes in Column Temperature

11. Mass Spectrometric Analysis of SOX11-Binding Proteins in Head and Neck Cancer Cells Demonstrates the Interaction of SOX11 and HSP90α

12. Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues

13. Quantitation of 87 Proteins by nLC-MRM/MS in Human Plasma: Workflow for Large-Scale Analysis of Biobank Samples

14. Therapeutic Mechanistic Studies of ShuFengJieDu Capsule in an Acute Lung Injury Animal Model Using Quantitative Proteomics Technology

15. Urine Metabonomics Reveals Early Biomarkers in Diabetic Cognitive Dysfunction

16. Virulent and Vaccine Strains of Streptococcus equi ssp. zooepidemicus Have Different Influences on Phagocytosis and Cytokine Secretion of Macrophages

17. A Surface Biotinylation Strategy for Reproducible Plasma Membrane Protein Purification and Tracking of Genetic and Drug-Induced Alterations

18. Analysis of Intrinsic Peptide Detectability via Integrated Label-Free and SRM-Based Absolute Quantitative Proteomics

19. BatMass: a Java Software Platform for LC–MS Data Visualization in Proteomics and Metabolomics

20. Differential Isotope Labeling of Glycopeptides for Accurate Determination of Differences in Site-Specific Glycosylation

21. Discovery, Synthesis, and Functional Characterization of a Novel Neuroprotective Natural Product from the Fruit of Alpinia oxyphylla for use in Parkinson’s Disease Through LC/MS-Based Multivariate Data Analysis-Guided Fractionation

22. Distinct Metabolic Signature of Human Bladder Cancer Cells Carrying an Impaired Fanconi Anemia Tumor-Suppressor Signaling Pathway

23. Fast and Reliable Quantitative Peptidomics with labelpepmatch

24. Fecal Metabolome in Hmga1 Transgenic Mice with Polyposis: Evidence for Potential Screen for Early Detection of Precursor Lesions in Colorectal Cancer

25. High-Throughput LC–MS/MS Proteomic Analysis of a Mouse Model of Mesiotemporal Lobe Epilepsy Predicts Microglial Activation Underlying Disease Development

26. Immunoproteomics-Based Analysis of the Immunocompetent Serological Response to Lomentospora prolificans

27. Integrated Proteomic Pipeline Using Multiple Search Engines for a Proteogenomic Study with a Controlled Protein False Discovery Rate

28. Nontargeted LC–MS Metabolomics Approach for Metabolic Profiling of Plasma and Urine from Pigs Fed Branched Chain Amino Acids for Maximum Growth Performance

29. Prediction of Protein Lysine Acylation by Integrating Primary Sequence Information with Multiple Functional Features

30. Proteome Differences between Hepatitis B Virus Genotype-B- and Genotype-C-Induced Hepatocellular Carcinoma Revealed by iTRAQ-Based Quantitative Proteomics

31. Proteomic Analysis of Human Tendon and Ligament: Solubilization and Analysis of Insoluble Extracellular Matrix in Connective Tissues

32. Proteomics Quality Control: Quality Control Software for MaxQuant Results

33. Targeted Metabolomic Pathway Analysis and Validation Revealed Glutamatergic Disorder in the Prefrontal Cortex among the Chronic Social Defeat Stress Mice Model of Depression

34. A Method for Comprehensive Glycosite-Mapping and Direct Quantitation of Serum Glycoproteins

35. ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC–MS/MS Experiments

36. Antibiotic Treatment Preventing Necrotising Enterocolitis Alters Urinary and Plasma Metabolomes in Preterm Pigs

37. Attached and Planktonic Listeria monocytogenes Global Proteomic Responses and Associated Influence of Strain Genetics and Temperature

38. Branched-Chain Amino Acids as Predictors for Individual Differences of Cisplatin Nephrotoxicity in Rats: A Pharmacometabonomics Study

39. Cartilaginous Metabolomic Study Reveals Potential Mechanisms of Osteophyte Formation in Osteoarthritis

40. Characterization of the Molecular Mechanisms Underlying the Chronic Phase of Stroke in a Cynomolgus Monkey Model of Induced Cerebral Ischemia

41. Combining De Novo Peptide Sequencing Algorithms, A Synergistic Approach to Boost Both Identifications and Confidence in Bottom-up Proteomics

42. Comparative Proteomic Analysis of Developing Rhizomes of the Ancient Vascular Plant Equisetum hyemale and Different Monocot Species

43. Comparative Proteomic Analysis of Wild-Type and SAP Domain Mutant Foot-and-Mouth Disease Virus-Infected Porcine Cells Identifies the Ubiquitin-Activating Enzyme UBE1 Required for Virus Replication

44. Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra

45. Comprehensive Metabolic Profiling of Age-Related Mitochondrial Dysfunction in the High-Fat-Fed ob/ob Mouse Heart

46. DIGESTIF: A Universal Quality Standard for the Control of Bottom-Up Proteomics Experiments

47. Deep Phosphotyrosine Proteomics by Optimization of Phosphotyrosine Enrichment and MS/MS Parameters

48. Development of Urinary Pseudotargeted LC-MS-Based Metabolomics Method and Its Application in Hepatocellular Carcinoma Biomarker Discovery

49. Development of a Postcolumn Infused-Internal Standard Liquid Chromatography Mass Spectrometry Method for Quantitative Metabolomics Studies

50. Differential Peptide Labeling (iTRAQ) in LC–MS/MS Based Proteomics in Daphnia Reveal Mechanisms of an Antipredator Response

51. Experimental Null Method to Guide the Development of Technical Procedures and to Control False-Positive Discovery in Quantitative Proteomics

52. Forecasting Chronic Diseases Using Data Fusion

53. Francisella tularensis LVS Surface and Membrane Proteins as Targets of Effective Post-Exposure Immunization for Tularemia

54. Gas Chromatography/Mass Spectrometry Metabolomics of Urine and Serum from Nonhuman Primates Exposed to Ionizing Radiation: Impacts on the Tricarboxylic Acid Cycle and Protein Metabolism

55. Glycoproteins in Claudin-Low Breast Cancer Cell Lines Have a Unique Expression Profile

56. Glycoproteomic Comparison of Clinical Triple-Negative and Luminal Breast Tumors

57. Hippocampal Proteomic and Metabonomic Abnormalities in Neurotransmission, Oxidative Stress, and Apoptotic Pathways in a Chronic Phencyclidine Rat Model

58. Identification of Proteomic Features To Distinguish Benign Pulmonary Nodules from Lung Adenocarcinoma

59. Kinobead and Single-Shot LC-MS Profiling Identifies Selective PKD Inhibitors

60. LC–MS Metabolomics of Psoriasis Patients Reveals Disease Severity-Dependent Increases in Circulating Amino Acids That Are Ameliorated by Anti-TNFα Treatment

61. Metabonomic Profiling Reveals Cancer Chemopreventive Effects of American Ginseng on Colon Carcinogenesis in ApcMin/+ Mice

62. Network Marker Selection for Untargeted LC–MS Metabolomics Data

63. Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements

64. Optimizing High-Resolution Mass Spectrometry for the Identification of Low-Abundance Post-Translational Modifications of Intact Proteins

65. Plasma Metabolite Biomarkers for the Detection of Pancreatic Cancer

66. Profiling of Acylcarnitines in First Episode Psychosis before and after Antipsychotic Treatment

67. Protein Quantification Using a Cleavable Reporter Peptide

68. Proteomics Analysis of EV71-Infected Cells Reveals the Involvement of Host Protein NEDD4L in EV71 Replication

69. Proteomics Provides Insight into the Interaction between Mulberry and Silkworm

70. Qualitative and Quantitative Analysis of Proteome and Peptidome of Human Follicular Fluid Using Multiple Samples from Single Donor with LC–MS and SWATH Methodology

92. Comparative Analysis of the Endogenous Peptidomes Displayed by HLA-B27 and Mamu-B08: Two MHC Class I Alleles Associated with Elite Control of HIV/SIV Infection