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You searched for: Journal name Journal of Proteome Research Remove constraint Journal name: Journal of Proteome Research Subject term liquid chromatography Remove constraint Subject term: liquid chromatography Text availability Citation in PubAg Remove constraint Text availability: Citation in PubAg
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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

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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

20. 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

21. 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

22. 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

23. 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

24. 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

25. 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

26. 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

27. 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

28. 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

29. 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

30. 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

31. 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

32. 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

33. 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

34. 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

35. 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

36. 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

37. 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

38. 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

39. 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

40. 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

41. 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

42. 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

43. 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

44. 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

45. 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

46. 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

47. 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

48. 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

49. 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

50. 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

51. 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

52. Comparative Analysis of the Endogenous Peptidomes Displayed by HLA-B*27 and Mamu-B*08: 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

53. 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

54. 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

55. 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

56. 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

57. 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

58. 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

59. 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

60. 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

61. High-Performance Chemical Isotope Labeling Liquid Chromatography–Mass Spectrometry for Profiling the Metabolomic Reprogramming Elicited by Ammonium Limitation in Yeast

Author:
Luo Xian; Zhao Shuang; Huan Tao; Sun Difei; Friis R. Magnus N.; Schultz Michael C.; Li Liang
Source:
Journal of Proteome Research 2016 v.15 no.5 pp. 1602-1612
ISSN:
1535-3907
Subject:
acetyl coenzyme A; ammonium; carbon; carboxylic acids; databases; fuels; isotope labeling; liquid chromatography; mass spectrometry; metabolic engineering; metabolism; metabolites; metabolome; metabolomics; phenol; proteome; stable isotopes; yeasts
Abstract:
... Information about how yeast metabolism is rewired in response to internal and external cues can inform the development of metabolic engineering strategies for food, fuel, and chemical production in this organism. We report a new metabolomics workflow for the characterization of such metabolic rewiring. The workflow combines efficient cell lysis without using chemicals that may interfere with downs ...
DOI:
10.1021/acs.jproteome.6b00070

62. High-Throughput Quantitative Lipidomics Analysis of Nonesterified Fatty Acids in Human Plasma

Author:
Christinat Nicolas; Morin-Rivron Delphine; Masoodi Mojgan
Source:
Journal of Proteome Research 2016 v.15 no.7 pp. 2228-2235
ISSN:
1535-3907
Subject:
EDTA (chelating agent); anticoagulants; carbon; fatty acid composition; free fatty acids; heparin; humans; isomers; liquid chromatography; mass spectrometry; omega-6 fatty acids; proteome; quantitative analysis; robots
Abstract:
... We present a high-throughput, nontargeted lipidomics approach using liquid chromatography coupled to high-resolution mass spectrometry for quantitative analysis of nonesterified fatty acids. We applied this method to screen a wide range of fatty acids from medium-chain to very long-chain (8 to 24 carbon atoms) in human plasma samples. The method enables us to chromatographically separate branched- ...
DOI:
10.1021/acs.jproteome.6b00198

63. 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

64. Identification and Characterization of Novel Chitin-Binding Proteins from the Larval Cuticle of Silkworm, Bombyx mori

Author:
Dong Zhaoming; Zhang Weiwei; Zhang Yan; Zhang Xiaolu; Zhao Ping; Xia Qingyou
Source:
Journal of Proteome Research 2016 v.15 no.5 pp. 1435-1445
ISSN:
1535-3907
Subject:
Bombyx mori; chitin; larvae; liquid chromatography; mechanical properties; proteins; proteome; silkworms; tandem mass spectrometry
Abstract:
... Cuticle is mainly made of chitin filaments embedded in a matrix of cuticular proteins (CPs). Cuticular chitins have minor differences, whereas CPs are widely variable with respect to their sequences and structures. To understand the molecular basis underlying the mechanical properties of cuticle, it is necessary to know which CPs interact with chitin and how they are assembled into the cuticle str ...
DOI:
10.1021/acs.jproteome.5b00943

65. LaCyTools: A Targeted Liquid Chromatography–Mass Spectrometry Data Processing Package for Relative Quantitation of Glycopeptides

Author:
Jansen Bas C.; Falck David; de Haan Noortje; Hipgrave Ederveen Agnes L.; Razdorov Genadij; Lauc Gordan; Wuhrer Manfred
Source:
Journal of Proteome Research 2016 v.15 no.7 pp. 2198-2210
ISSN:
1535-3907
Subject:
computer software; glycopeptides; glycoproteomics; glycosylation; information processing; liquid chromatography; mass spectrometry; proteome; statistical analysis
Abstract:
... Bottom-up glycoproteomics by liquid chromatography–mass spectrometry (LC–MS) is an established approach for assessing glycosylation in a protein- and site-specific manner. Consequently, tools are needed to automatically align, calibrate, and integrate LC–MS glycoproteomics data. We developed a modular software package designed to tackle the individual aspects of an LC–MS experiment, called LaCyToo ...
DOI:
10.1021/acs.jproteome.6b00171

66. Lipidomic Perturbations in Lung, Kidney, and Liver Tissues of p53 Knockout Mice Analyzed by Nanoflow UPLC-ESI-MS/MS

Author:
Park Se Mi; Byeon Seul Kee; Sung Hyerim; Cho Soo Young; Seong Je Kyung; Moon Myeong Hee
Source:
Journal of Proteome Research 2016 v.15 no.10 pp. 3763-3772
ISSN:
1535-3907
Subject:
carcinogenesis; diacylglycerols; genes; kidneys; knockout mutants; lipid composition; liquid chromatography; liver; lungs; mice; mutation; neoplasms; phosphatidylcholines; phosphatidylethanolamines; phosphatidylserines; proteome; quantitative analysis; sphingomyelins; tandem mass spectrometry; tissues; triacylglycerols
Abstract:
... Lipids are important signaling molecules regulating biological processes under normal and diseased conditions. Although p53 mutation is well-known for causing cancer, the relationship between p53-related tumorigenesis and altered lipid profile is unclear. We profiled differences in lipid expressions in liver, lung, and kidney in p53 knockout (KO) mice by high-speed quantitative analysis of 320 lip ...
DOI:
10.1021/acs.jproteome.6b00566

67. Mass-Spectrometry-Based Quantification of Protein-Bound Fatty Acid Synthesis Intermediates from Escherichia coli

Author:
Noga Marek J.; Cerri Mattia; Imholz Nicole; Tulinski Pawel; Şahin Enes; Bokinsky Gregory
Source:
Journal of Proteome Research 2016 v.15 no.10 pp. 3617-3623
ISSN:
1535-3907
Subject:
Escherichia coli; acyl carrier protein; antibiotics; biochemical pathways; biosynthesis; biotechnology; cerulenin; fatty acids; ionization; liquid chromatography; mass spectrometry; microbial physiology; models; nutrients; proteome; statistical analysis
Abstract:
... The production of fatty acids from simple nutrients occurs via a complex biosynthetic pathway with dozens of intermediate compounds and multiple branch points. Despite its importance for microbial physiology and biotechnology, critical aspects of fatty acid biosynthesis, especially dynamics of in vivo regulation, remain poorly characterized. We have developed a liquid chromatography/mass spectrosc ...
DOI:
10.1021/acs.jproteome.6b00405

68. Metabolomic Analysis of Gastric Cancer Progression within the Correa’s Cascade Using Ultraperformance Liquid Chromatography–Mass Spectrometry

Author:
Kuligowski Julia; Sanjuan-Herráez Daniel; Vázquez-Sánchez María A.; Brunet-Vega Anna; Pericay Carles; Ramírez-Lázaro María José; Lario Sergio; Gombau Lourdes; Junquera Félix; Calvet Xavier; Quintás Guillermo
Source:
Journal of Proteome Research 2016 v.15 no.8 pp. 2729-2738
ISSN:
1535-3907
Subject:
Correa; Helicobacter pylori; adenocarcinoma; atrophy; biomarkers; carcinogenesis; disease course; gastritis; indoleamine 2,3-dioxygenase; kynurenine; liquid chromatography; mass spectrometry; metabolites; metaplasia; models; patients; proteome; stomach neoplasms; tryptophan
Abstract:
... Gastric cancer (GC) is among the most common cancers worldwide. Gastric carcinogenesis is a multistep and multifactorial process beginning with chronic gastritis induced by Helicobacter pylori (H. pylori) infection. This process is often described via a sequence of events known as Correas’s cascade, a stepwise progression from nonactive gastritis, chronic active gastritis, precursor lesions of gas ...
DOI:
10.1021/acs.jproteome.6b00281

69. Plasma Lipidomics Investigation of Hemodialysis Effects by Using Liquid Chromatography–Mass Spectrometry

Author:
Wang Lichao; Hu Chunxiu; Liu Shuxin; Chang Ming; Gao Peng; Wang Lili; Pan Zaifa; Xu Guowang
Source:
Journal of Proteome Research 2016 v.15 no.6 pp. 1986-1994
ISSN:
1535-3907
Subject:
blood lipids; eicosanoids; free fatty acids; hemodialysis; humans; lipid metabolism; liquid chromatography; liquids; mass spectrometry; patients; proteome; risk; uremia
Abstract:
... Chronic kidney disease (CKD) has been a global health problem that has a great possibility of being developed into uremia in the end. Hemodialysis (HD) is the most commonly used strategy for treating uremic patients; however, the patients still have a high risk of suffering various complications. It is well recognized that lipid disorder usually occurs in maintenance HD patients. To systemically s ...
DOI:
10.1021/acs.jproteome.6b00170

70. Progressive Changes in the Plasma Metabolome during Malnutrition in Juvenile Pigs

Author:
Jiang Pingping; Stanstrup Jan; Thymann Thomas; Sangild Per Torp; Dragsted Lars Ove
Source:
Journal of Proteome Research 2016 v.15 no.2 pp. 447-456
ISSN:
1535-3907
Subject:
amino acids; body weight changes; children; choline; corn; death; diet; diet therapy; digestive system; disease course; foods; juveniles; liquid chromatography; malnutrition; mass spectrometry; metabolism; metabolites; metabolome; metabolomics; models; physiological state; piglets; proteome; refeeding
Abstract:
... Severe acute malnutrition (SAM) is one of the leading nutrition-related causes of death in children under five years of age. The clinical features of SAM are well documented, but a comprehensive understanding of the development from a normal physiological state to SAM is lacking. Characterizing the temporal metabolomic change may help to understand the disease progression and to define nutritional ...
DOI:
10.1021/acs.jproteome.5b00782

71. 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

72. Proteome-wide Lysine Glutarylation Profiling of the Mycobacterium tuberculosis H37Rv

Author:
Xie Longxiang; Wang Guirong; Yu Zhaoxiao; Zhou Mingliang; Li Qiming; Huang Hairong; Xie Jianping
Source:
Journal of Proteome Research 2016 v.15 no.4 pp. 1379-1385
ISSN:
1535-3907
Subject:
Escherichia coli; Mycobacterium tuberculosis; antibodies; eukaryotic cells; liquid chromatography; lysine; mass spectrometry; pathogenesis; post-translational modification; proteome; ribosomal proteins; transferases
Abstract:
... Lysine glutarylation, a new protein posttranslational modification (PTM), was recently identified and characterized in both prokaryotic and eukaryotic cells. To explore the distribution of lysine glutarylation in Mycobacterium tuberculsosis, by using a comprehensive method combining the immune affinity peptide enrichment by the glutaryl-lysine antibody with LC–MS, we finally identified 41 glutaryl ...
DOI:
10.1021/acs.jproteome.5b00917

73. Proteomic Investigation of Ram Spermatozoa and the Proteins Conferred by Seminal Plasma

Author:
Pini Taylor; Leahy Tamara; Soleilhavoup Clement; Tsikis Guillaume; Labas Valerie; Combes-Soia Lucie; Harichaux Gregoire; Rickard Jessica P.; Druart Xavier; de Graaf Simon P.
Source:
Journal of Proteome Research 2016 v.15 no.10 pp. 3700-3711
ISSN:
1535-3907
Subject:
biochemical pathways; epididymis; genes; insemination; liquid chromatography; liver; plasma membrane; proteins; proteome; proteomics; rams; seminal plasma; spermatozoa; tandem mass spectrometry
Abstract:
... Sperm proteomes have emerged for several species; however, the extent of species similarity is unknown. Sheep are an important agricultural species for which a comprehensive sperm proteome has not been produced. In addition, potential proteomic factors from seminal plasma that may contribute to improved fertility after cervical insemination are yet to be explored. Here we use liquid chromatography ...
DOI:
10.1021/acs.jproteome.6b00530

74. Proteomic Profile of Unstable Atheroma Plaque: Increased Neutrophil Defensin 1, Clusterin, and Apolipoprotein E Levels in Carotid Secretome

Author:
Aragonès Gemma; Auguet Teresa; Guiu-Jurado Esther; Berlanga Alba; Curriu Marta; Martinez Salomé; Alibalic Ajla; Aguilar Carmen; Hernández Esteban; Camara María-Luisa; Canela Núria; Herrero Pol; Ruyra Xavier; Martín-Paredero Vicente; Richart Cristóbal
Source:
Journal of Proteome Research 2016 v.15 no.3 pp. 933-944
ISSN:
1535-3907
Subject:
apolipoprotein E; atherosclerosis; biomarkers; enzyme-linked immunosorbent assay; focal adhesions; liquid chromatography; mass spectrometry; neutrophils; protein secretion; proteome; proteomics
Abstract:
... Because of the clinical significance of carotid atherosclerosis, the search for novel biomarkers has become a priority. The aim of the present study was to compare the protein secretion profile of the carotid atherosclerotic plaque (CAP, n = 12) and nonatherosclerotic mammary artery (MA, n = 10) secretomes. We used a nontargeted proteomic approach that incorporated tandem immunoaffinity depletion, ...
DOI:
10.1021/acs.jproteome.5b00936

75. 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

76. 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

77. 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

78. 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

79. Untargeted Metabolomics Analysis Reveals a Link between ETHE1-Mediated Disruptive Redox State and Altered Metabolic Regulation

Author:
Sahebekhtiari Navid; Nielsen Camilla Bak; Johannsen Mogens; Palmfeldt Johan
Source:
Journal of Proteome Research 2016 v.15 no.5 pp. 1630-1638
ISSN:
1535-3907
Subject:
NAD (coenzyme); amino acids; brain; encephalopathy; fibroblasts; genes; glutathione; inherited metabolic diseases; liquid chromatography; metabolites; metabolomics; pantothenic acid; patients; phenotype; physiology; proteome; tricarboxylic acid cycle
Abstract:
... Defects in the gene encoding the persulfide dioxygenase ETHE1 are known to cause the severe inherited metabolic disorder ethylmalonic encephalopathy (EE). In spite of known clinical characteristics, the molecular mechanisms underlying the ETHE1 deficiency are still obscure. Herein, to further analyze the molecular phenotype of the disease, we applied an untargeted metabolomics approach on cultivat ...
DOI:
10.1021/acs.jproteome.6b00100

80. Untargeted Metabolomics Analysis of ABCC6-Deficient Mice Discloses an Altered Metabolic Liver Profile

Author:
Rasmussen Mie R.; Nielsen Kirstine L.; Laursen Mia R.; Nielsen Camilla B.; Svendsen Pia; Dimke Henrik; Christensen Erik I.; Johannsen Mogens; Moestrup Søren K.
Source:
Journal of Proteome Research 2016 v.15 no.12 pp. 4591-4600
ISSN:
1535-3907
Subject:
acetylation; amino acids; cytosol; eyes; genes; liquid chromatography; liver; mass spectrometry; metabolic diseases; metabolites; metabolomics; mice; mineralization; pantothenic acid; proteome; tissues; transport proteins; urine
Abstract:
... Loss-of-function mutations in the transmembrane ABCC6 transport protein cause pseudoxanthoma elasticum (PXE), an ectopic, metabolic mineralization disorder that affects the skin, eye, and vessels. ABCC6 is assumed to mediate efflux of one or several small molecule compounds from the liver cytosol to the circulation. Untargeted metabolomics using liquid chromatography−mass spectrometry was employed ...
DOI:
10.1021/acs.jproteome.6b00669

81. 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

82. A Pharmacometabonomic Approach To Predicting Metabolic Phenotypes and Pharmacokinetic Parameters of Atorvastatin in Healthy Volunteers

Author:
Huang Qing; Aa Jiye; Jia Huning; Xin Xiaoqing; Tao Chunlei; Liu Linsheng; Zou Bingjie; Song Qinxin; Shi Jian; Cao Bei; Yong Yonghong; Wang Guangji; Zhou Guohua
Source:
Journal of Proteome Research 2015 v.14 no.9 pp. 3970-3981
ISSN:
1535-3907
Subject:
alanine; arachidonic acid; cholesterol; drug therapy; drugs; gas chromatography-mass spectrometry; genetic polymorphism; isoleucine; least squares; liquid chromatography; metabolites; metabolomics; models; pharmacokinetics; phenotype; prediction; proteome; tandem mass spectrometry; toxicity; tryptophan
Abstract:
... Genetic polymorphism and environment each influence individual variability in drug metabolism and disposition. It is preferable to predict such variability, which may affect drug efficacy and toxicity, before drug administration. We examined individual differences in the pharmacokinetics of atorvastatin by applying gas chromatography–mass spectrometry-based metabolic profiling to predose plasma sa ...
DOI:
10.1021/acs.jproteome.5b00440

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

84. Alterations in Human Liver Metabolome during Prolonged Cryostorage

Author:
Abuja Peter M.; Ehrhart Friederike; Schoen Uwe; Schmidt Tomm; Stracke Frank; Dallmann Guido; Friedrich Torben; Zimmermann Heiko; Zatloukal Kurt
Source:
Journal of Proteome Research 2015 v.14 no.7 pp. 2758-2768
ISSN:
1535-3907
Subject:
ambient temperature; freezers; humans; hydrolysis; lipids; liquid chromatography; liquids; liver; mass spectrometry; metabolites; metabolome; metabolomics; nitrogen; peptides; proteome; storage temperature
Abstract:
... Tissue metabolomics requires high sample quality that crucially depends on the biobanking storage protocol. Hence, we systematically analyzed the influence of realistic storage scenarios on the liver metabolome with different storage temperatures and repeated transfer of samples between storage and retrieval environments, simulating the repeated temperature changes affecting unrelated samples stor ...
DOI:
10.1021/acs.jproteome.5b00025

85. An Integrated Workflow for Multiplex CSF Proteomics and PeptidomicsIdentification of Candidate Cerebrospinal Fluid Biomarkers of Alzheimer’s Disease

Author:
Hölttä Mikko; Minthon Lennart; Hansson Oskar; Holmén-Larsson Jessica; Pike Ian; Ward Malcolm; Kuhn Karsten; Rüetschi Ulla; Zetterberg Henrik; Blennow Kaj; Gobom Johan
Source:
Journal of Proteome Research 2015 v.14 no.2 pp. 654-663
ISSN:
1535-3907
Subject:
Alzheimer disease; biomarkers; brain; cerebrospinal fluid; filters; liquid chromatography; mass spectrometry; membrane proteins; patients; peptides; protein composition; proteome; proteomics; ultrafiltration
Abstract:
... Many disease processes in the brain are reflected in the protein composition of the cerebrospinal fluid (CSF). In addition to proteins, CSF also contains a large number of endogenous peptides whose potential as disease biomarkers largely remains to be explored. We have developed a novel workflow in which multiplex isobaric labeling is used for simultaneous quantification of endogenous CSF peptides ...
DOI:
10.1021/pr501076j

86. Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses

Author:
Thévenot Etienne A.; Roux Aurélie; Xu Ying; Ezan Eric; Junot Christophe
Source:
Journal of Proteome Research 2015 v.14 no.8 pp. 3322-3335
ISSN:
1535-3907
Subject:
adults; biomarkers; body mass index; cohort studies; correlation; databases; gender; least squares; liquid chromatography; mass spectrometry; medicine; metabolites; metabolome; metabolomics; models; proteome; toxicology; urine
Abstract:
... Urine metabolomics is widely used for biomarker research in the fields of medicine and toxicology. As a consequence, characterization of the variations of the urine metabolome under basal conditions becomes critical in order to avoid confounding effects in cohort studies. Such physiological information is however very scarce in the literature and in metabolomics databases so far. Here we studied t ...
DOI:
10.1021/acs.jproteome.5b00354

87. Annotation of the Staphylococcus aureus Metabolome Using Liquid Chromatography Coupled to High-Resolution Mass Spectrometry and Application to the Study of Methicillin Resistance

Author:
Aros-Calt Sandrine; Muller Bruno H.; Boudah Samia; Ducruix Céline; Gervasi Gaspard; Junot Christophe; Fenaille François
Source:
Journal of Proteome Research 2015 v.14 no.11 pp. 4863-4875
ISSN:
1535-3907
Subject:
Staphylococcus aureus; antibiotic resistance; biosynthesis; databases; developmental stages; hydrophilic interaction chromatography; mass spectrometry; metabolites; metabolome; metabolomics; methicillin; pathogens; peptidoglycans
Abstract:
... Staphylococcus aureus can cause a variety of severe disease patterns and can readily acquire antibiotic resistance; however, the mechanisms by which this commensal becomes a pathogen or develops antibiotic resistance are still poorly understood. Here we asked whether metabolomics can be used to distinguish bacterial strains with different antibiotic susceptibilities. Thus, an efficient and robust ...
DOI:
10.1021/acs.jproteome.5b00697

88. 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

89. Combined High-Density Lipoprotein Proteomic and Glycomic Profiles in Patients at Risk for Coronary Artery Disease

Author:
Krishnan Sridevi; Huang Jincui; Lee Hyeyoung; Guerrero Andres; Berglund Lars; Anuurad Erdembileg; Lebrilla Carlito B.; Zivkovic Angela M.
Source:
Journal of Proteome Research 2015 v.14 no.12 pp. 5109-5118
ISSN:
1535-3907
Subject:
amyloid; angiography; atherosclerosis; biomarkers; blood serum; coronary artery disease; gangliosides; glycomics; high density lipoprotein; liquid chromatography; mass spectrometry; multivariate analysis; patients; polysaccharides; principal component analysis; proteome; proteomics; risk; ultracentrifugation
Abstract:
... Objectives: To test whether recently developed methods for comprehensive profiling of the high-density lipoprotein (HDL) glycome combined with the HDL proteome can distinguish individuals with coronary artery disease (CAD) from those without. Methods: Twenty subjects at risk for CAD, who underwent diagnostic coronary arteriography, were analyzed. Ten subjects had CAD, and ten did not. HDL was extr ...
DOI:
10.1021/acs.jproteome.5b00730

90. Data Processing Has Major Impact on the Outcome of Quantitative Label-Free LC-MS Analysis

Author:
Chawade Aakash; Sandin Marianne; Teleman Johan; Malmström Johan; Levander Fredrik
Source:
Journal of Proteome Research 2015 v.14 no.2 pp. 676-687
ISSN:
1535-3907
Subject:
algorithms; computer software; data collection; information processing; liquid chromatography; mass spectrometry; monitoring; proteome; statistical analysis; synthetic peptides
Abstract:
... High-throughput multiplexed protein quantification using mass spectrometry is steadily increasing in popularity, with the two major techniques being data-dependent acquisition (DDA) and targeted acquisition using selected reaction monitoring (SRM). However, both techniques involve extensive data processing, which can be performed by a multitude of different software solutions. Analysis of quantita ...
DOI:
10.1021/pr500665j

91. Development of Phage-Based Antibody Fragment Reagents for Affinity Enrichment of Bacterial Immunoglobulin G Binding Proteins

Author:
Säll Anna; Sjöholm Kristoffer; Waldemarson Sofia; Happonen Lotta; Karlsson Christofer; Persson Helena; Malmström Johan
Source:
Journal of Proteome Research 2015 v.14 no.11 pp. 4704-4713
ISSN:
1535-3907
Subject:
Streptococcus pyogenes; antibodies; bacterial infections; binding capacity; binding proteins; death; humans; immunoglobulin G; liquid chromatography; mass spectrometry; monitoring; proteome; surface proteins; virulence
Abstract:
... Disease and death caused by bacterial infections are global health problems. Effective bacterial strategies are required to promote survival and proliferation within a human host, and it is important to explore how this adaption occurs. However, the detection and quantification of bacterial virulence factors in complex biological samples are technically demanding challenges. These can be addressed ...
DOI:
10.1021/acs.jproteome.5b00585

92. Distinct Metabolomic Profiles of Papillary Thyroid Carcinoma and Benign Thyroid Adenoma

Author:
Xu Yanan; Zheng Xiaojiao; Qiu Yunping; Jia Wei; Wang Jiadong; Yin Shankai
Source:
Journal of Proteome Research 2015 v.14 no.8 pp. 3315-3321
ISSN:
1535-3907
Subject:
adenoma; amino acid metabolism; bile acids; carbon metabolism; carcinogenesis; carcinoma; fatty acids; glycolysis; head; liquid chromatography; liquids; mass spectrometry; metabolites; metabolomics; neck; patients; proteome; taurine; thyroid neoplasms; tissues; tryptophan
Abstract:
... Papillary thyroid carcinoma (PTC) and benign thyroid adenoma (BTA) are the most common head and neck tumors. However, the metabolic differences between PTC and BTA have not been characterized. The aim of this study was to identify the metabolic profiles of these two types of tumors using a metabolomics approach. Tumors and adjacent nontumor specimens collected from 57 patients with PTC and 48 pati ...
DOI:
10.1021/acs.jproteome.5b00351

93. 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

94. FAIMS and Phosphoproteomics of Fibroblast Growth Factor Signaling: Enhanced Identification of Multiply Phosphorylated Peptides

Author:
Zhao Hongyan; Cunningham Debbie L.; Creese Andrew J.; Heath John K.; Cooper Helen J.
Source:
Journal of Proteome Research 2015 v.14 no.12 pp. 5077-5087
ISSN:
1535-3907
Subject:
enzyme inhibitors; fibroblast growth factor receptors; fibroblast growth factors; liquid chromatography; phosphopeptides; phosphorylation; proteome; proteomics; tandem mass spectrometry
Abstract:
... We have applied liquid chromatography high-field asymmetric waveform ion mobility spectrometry tandem mass spectrometry (LC–FAIMS–MS/MS) and liquid chromatography tandem mass spectrometry (LC–MS/MS) to the investigation of site-specific phosphorylation in fibroblast growth factor (FGF) signaling. We have combined a SILAC approach with chemical inhibition by SU5402 (an FGF receptor tyrosine kinase ...
DOI:
10.1021/acs.jproteome.5b00713

95. First Succinyl-Proteome Profiling of Extensively Drug-Resistant Mycobacterium tuberculosis Revealed Involvement of Succinylation in Cellular Physiology

Author:
Xie Longxiang; Liu Wei; Li Qiming; Chen Shudan; Xu Mengmeng; Huang Qinqin; Zeng Jie; Zhou Mingliang; Xie Jianping
Source:
Journal of Proteome Research 2015 v.14 no.1 pp. 107-119
ISSN:
1535-3907
Subject:
Escherichia coli; Mycobacterium tuberculosis; acetylation; active sites; antibiotic resistance; bioinformatics; carbon metabolism; enzymes; liquid chromatography; lysine; post-translational modification; prokaryotic cells; proteins; proteome; stress response; tandem mass spectrometry; translation (genetics)
Abstract:
... Protein lysine succinylation, an emerging protein post-translational modification widespread among eukaryotic and prokaryotic cells, represents an important regulator of cellular processes. However, the extent and function of lysine succinylation in Mycobacterium tuberculosis, especially extensively drug-resistant strain, remain elusive. Combining protein/peptide prefractionation, immunoaffinity e ...
DOI:
10.1021/pr500859a

96. 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

97. Global Analysis of Protein Lysine Succinylation Profiles and Their Overlap with Lysine Acetylation in the Marine Bacterium Vibrio parahemolyticus

Author:
Pan Jianyi; Chen Ran; Li Chuchu; Li Weiyan; Ye Zhicang
Source:
Journal of Proteome Research 2015 v.14 no.10 pp. 4309-4318
ISSN:
1535-3907
Subject:
Vibrio parahaemolyticus; acetylation; aquatic bacteria; arginine; bioinformatics; eukaryotic cells; liquid chromatography; lysine; models; peptides; post-translational modification; proteins; proteome; tandem mass spectrometry
Abstract:
... Protein lysine acylation, including acetylation and succinylation, has been found to be a major post-translational modification (PTM) and is associated with the regulation of cellular processes that are widespread in bacteria. Vibrio parahemolyticus is a model marine bacterium that causes seafood-borne illness in humans worldwide. The lysine acetylation of V. parahemolyticus has been extensively c ...
DOI:
10.1021/acs.jproteome.5b00485

98. Global Phosphoproteomic Analysis of Daphnia pulex Reveals Evolutionary Conservation of Ser/Thr/Tyr Phosphorylation

Author:
Kwon Oh Kwang; Sim JuHee; Yun Ki Na; Kim Jin Young; Lee Sangkyu
Source:
Journal of Proteome Research 2014 v.13 no.3 pp. 1327-1335
ISSN:
1535-3907
Subject:
Daphnia pulex; catalytic activity; ecotoxicology; eukaryotic cells; gene ontology; humans; liquid chromatography; mass spectrometry; membrane proteins; models; phosphopeptides; phosphoproteins; phosphorylation; plankton; prokaryotic cells; proteome; proteomics; screening; serine; threonine; titanium dioxide; tyrosine
Abstract:
... Reversible protein phosphorylations of serine, threonine, and tyrosine are critical processes in organisms ranging from prokaryotes to eukaryotes. Water fleas (Daphnids) have been used widely in ecologic and ecotoxicological studies, with more than 80% of ecotoxicological publications over the last 10 years involving planktonic genera, including Daphnia. However, the substrate proteins and the fun ...
DOI:
10.1021/pr400911x

99. Glycosylation of Human Plasma Clusterin Yields a Novel Candidate Biomarker of Alzheimer’s Disease

Author:
Liang Hui-Chung; Russell Claire; Mitra Vikram; Chung Raymond; Hye Abdul; Bazenet Chantal; Lovestone Simon; Pike Ian; Ward Malcolm
Source:
Journal of Proteome Research 2015 v.14 no.12 pp. 5063-5076
ISSN:
1535-3907
Subject:
Alzheimer disease; atrophy; biomarkers; glycopeptides; glycoproteomics; glycosylation; humans; liquid chromatography; patients; polysaccharides; tandem mass spectrometry
Abstract:
... Specific glycosylated peptides of clusterin are found associated with hippocampal atrophy. The glycosylation of clusterin from human plasma was comprehensively analyzed and characterized using mass spectrometry (MS)-based glycoproteomics analysis. All six known N-glycosylation sites are covered, three in the alpha subunit (α64N, α81N and α123N) and three in the beta subunit (β64N, β127N, and β147N ...
DOI:
10.1021/acs.jproteome.5b00892

100. Heat-Treatment-Responsive Proteins in Different Developmental Stages of Tomato Pollen Detected by Targeted Mass Accuracy Precursor Alignment (tMAPA)

Author:
Chaturvedi Palak; Doerfler Hannes; Jegadeesan Sridharan; Ghatak Arindam; Pressman Etan; Castillejo Maria Angeles; Wienkoop Stefanie; Egelhofer Volker; Firon Nurit; Weckwerth Wolfram
Source:
Journal of Proteome Research 2015 v.14 no.11 pp. 4463-4471
ISSN:
1535-3907
Subject:
Solanum lycopersicum var. lycopersicum; algorithms; developmental stages; fruit set; heat treatment; ions; liquid chromatography; mass spectrometry; pollen; protein isoforms; proteins; proteome; proteomics; tomatoes
Abstract:
... Recently, we have developed a quantitative shotgun proteomics strategy called mass accuracy precursor alignment (MAPA). The MAPA algorithm uses high mass accuracy to bin mass-to-charge (m/z) ratios of precursor ions from LC–MS analyses, determines their intensities, and extracts a quantitative sample versus m/z ratio data alignment matrix from a multitude of samples. Here, we introduce a novel fea ...
DOI:
10.1021/pr501240n