Journal name: Journal of Proteome Research / Text availability: Citation in PubAg

1. A Computational Selection of Metabolite Biomarkers Using Emerging Pattern Mining: A Case Study in Human Hepatocellular Carcinoma

Author:: Poezevara Guillaume; Lozano Sylvain; Cuissart Bertrand; Bureau Ronan; Bureau Pierre; Croixmarie Vincent; Vayer Philippe; Lepailleur Alban
Source:: Journal of Proteome Research 2017 v.16 no.6 pp. 2240-2249
ISSN:: 1535-3907
Subject:: biomarkers; case studies; data collection; diagnostic techniques; hepatoma; humans; metabolites; metabolomics; patients; proteome
Abstract:: ... The biomarker development in metabolomics aims at discriminating diseased from normal subjects and at creating a predictive model that can be used to diagnose new subjects. From a case study on human hepatocellular carcinoma (HCC), we studied for the first time the potential usefulness of the emerging patterns (EPs) that come from the data mining domain. When applied to a metabolomics data set lab ...
DOI:: 10.1021/acs.jproteome.7b00054
: https://doi.org/10.1021/acs.jproteome.7b00054

2. A Shotgun Proteomics Approach Reveals a New Toxic Role for Alzheimer’s Disease Aβ Peptide: Spliceosome Impairment

Author:: Nuzzo Domenico; Inguglia Luigi; Walters Jessica; Picone Pasquale; Di Carlo Marta
Source:: Journal of Proteome Research 2017 v.16 no.4 pp. 1526-1541
ISSN:: 1535-3907
Subject:: Alzheimer disease; Western blotting; biogenesis; bioinformatics; cytoskeleton; models; neurodegenerative diseases; pathogenesis; proteins; proteome; proteomics; spliceosomes; toxicity
Abstract:: ... Proteomic changes have been described in many neurodegenerative diseases, including Alzheimer’s disease (AD). However, the early events in the onset of the pathology are yet to be fully elucidated. A cell model system in which LAN5 neuroblastoma cells were incubated for a short time with a recombinant form of Aβ₄₂ was utilized. Proteins extracted from these cells were subjected to shotgun proteomi ...
DOI:: 10.1021/acs.jproteome.6b00925
: https://doi.org/10.1021/acs.jproteome.6b00925

3. Absolute Quantification of Human Milk Caseins and the Whey/Casein Ratio during the First Year of Lactation

Author:: Liao Yalin; Weber Darren; Xu Wei; Durbin-Johnson Blythe P.; Phinney Brett S.; Lönnerdal Bo
Source:: Journal of Proteome Research 2017 v.16 no.11 pp. 4113-4121
ISSN:: 1535-3907
Subject:: alpha-casein; amino acid composition; beta-casein; bioactive properties; breast milk; cattle; infant formulas; kappa-casein; lactation; protein content; proteome; quantitative analysis; regression analysis; whey; whey protein
Abstract:: ... Whey proteins and caseins in breast milk provide bioactivities and also have different amino acid composition. Accurate determination of these two major protein classes provides a better understanding of human milk composition and function, and further aids in developing improved infant formulas based on bovine whey proteins and caseins. In this study, we implemented a LC-MS/MS quantitative analys ...
DOI:: 10.1021/acs.jproteome.7b00486
: https://doi.org/10.1021/acs.jproteome.7b00486

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

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

5. Acute Consumption of Flavan-3-ol-Enriched Dark Chocolate Affects Human Endogenous Metabolism

Author:: Ostertag Luisa M.; Philo Mark; Colquhoun Ian J.; Tapp Henri S.; Saha Shikha; Duthie Garry G.; Kemsley E. Kate; de Roos Baukje; Kroon Paul A.; Le Gall Gwénaëlle
Source:: Journal of Proteome Research 2017 v.16 no.7 pp. 2516-2526
ISSN:: 1535-3907
Subject:: acute effects; amino acids; blood plasma; creatinine; flavanols; human health; humans; lactic acid; metabolism; metabolites; metabolome; metabolomics; multivariate analysis; nuclear magnetic resonance spectroscopy; proteome; pyruvic acid; risk; urine; white chocolate
Abstract:: ... Flavan-3-ols and methylxanthines have potential beneficial effects on human health including reducing cardiovascular risk. We performed a randomized controlled crossover intervention trial to assess the acute effects of consumption of flavan-3-ol-enriched dark chocolate, compared with standard dark chocolate and white chocolate, on the human metabolome. We assessed the metabolome in urine and bloo ...
DOI:: 10.1021/acs.jproteome.7b00089
: https://doi.org/10.1021/acs.jproteome.7b00089

6. Alterations in the Salivary Proteome and N-Glycome of Sjögren’s Syndrome Patients

Author:: Hall Steven C.; Hassis Maria E.; Williams Katherine E.; Albertolle Matthew E.; Prakobphol Akraporn; Dykstra Andrew B.; Laurance Megan; Ona Katherine; Niles Richard K.; Prasad Namrata; Gormley Matthew; Shiboski Caroline; Criswell Lindsey A.; Witkowska H. Ewa; Fisher Susan J.
Source:: Journal of Proteome Research 2017 v.16 no.4 pp. 1693-1705
ISSN:: 1535-3907
Subject:: Aleuria; agglutinins; biomarkers; carbonate dehydratase; fucose; glucosamine; glycopeptides; glycoproteins; glycosylation; histones; lectins; mass spectrometry; patients; permeability; proteome; saliva; wheat germ
Abstract:: ... We used isobaric mass tagging (iTRAQ) and lectin affinity capture mass spectrometry (MS)-based workflows for global analyses of parotid saliva (PS) and whole saliva (WS) samples obtained from patients diagnosed with primary Sjögren’s Syndrome (pSS) who were enrolled in the Sjögren’s International Collaborative Clinical Alliance (SICCA) as compared with two control groups. The iTRAQ analyses reve ...
DOI:: 10.1021/acs.jproteome.6b01051
: https://doi.org/10.1021/acs.jproteome.6b01051

7. Aminoquinoline Fluorescent Labels Obstruct Efficient Removal of N-Glycan Core α(1–6) Fucose by Bovine Kidney α-l-Fucosidase (BKF)

Author:: O’Flaherty Róisín; Harbison Aoife M.; Hanley Philip J.; Taron Christopher H.; Fadda Elisa; Rudd Pauline M.
Source:: Journal of Proteome Research 2017 v.16 no.11 pp. 4237-4243
ISSN:: 1535-3907
Subject:: Gibbs free energy; alpha-L-fucosidase; ambient temperature; binding sites; cattle; digestion; fucose; kidneys; proteome
Abstract:: ... Here we report evidence that new aminoquinoline N-glycan fluorescent labels interfere with the release of core α(1–6) fucose from N-glycans by bovine kidney α-l-fucosidase (BKF). BKF is a commonly employed exoglycosidase for core α(1–6) fucose determination. Molecular simulations of the bound and unbound Fuc-α(1–6)-GlcNAc, where GlcNAc is situated at the reducing end for all N-glycans, suggest tha ...
DOI:: 10.1021/acs.jproteome.7b00580
: https://doi.org/10.1021/acs.jproteome.7b00580

8. Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins

Author:: Skogs Marie; Stadler Charlotte; Schutten Rutger; Hjelmare Martin; Gnann Christian; Björk Lars; Poser Ina; Hyman Anthony; Uhlén Mathias; Lundberg Emma
Source:: Journal of Proteome Research 2017 v.16 no.1 pp. 147-155
ISSN:: 1535-3907
Subject:: antibodies; cell lines; fluorescent antibody technique; genes; proteins; proteome
Abstract:: ... Antibodies are indispensible research tools, yet the scientific community has not adopted standardized procedures to validate their specificity. Here we present a strategy to systematically validate antibodies for immunofluorescence (IF) applications using gene tagging. We have assessed the on- and off-target binding capabilities of 197 antibodies using 108 cell lines expressing EGFP-tagged target ...
DOI:: 10.1021/acs.jproteome.6b00821
: https://doi.org/10.1021/acs.jproteome.6b00821

9. Application of Metabolic Profiling to Abdominal Aortic Aneurysm Research

Author:: Qureshi Mahim I.; Greco Michele; Vorkas Panagiotis A.; Holmes Elaine; Davies Alun H.
Source:: Journal of Proteome Research 2017 v.16 no.7 pp. 2325-2332
ISSN:: 1535-3907
Subject:: aneurysm; biomarkers; blood serum; glycerol; humans; inflammation; lipid composition; lipid metabolism; metabolites; metabolomics; models; pathogenesis; proteome; risk; surgery; systematic review
Abstract:: ... Abdominal aortic aneurysm (AAA) is a complex disease posing diagnostic and therapeutic challenges. Metabonomics may aid in the diagnosis of AAA, determination of individualized risk, discovery of therapeutic targets, and improve understanding of pathogenesis. A systematic review of the diversity and outcomes of existing AAA metabonomic research has been performed. Original research studies applyin ...
DOI:: 10.1021/acs.jproteome.6b00894
: https://doi.org/10.1021/acs.jproteome.6b00894

10. Application of Nanosecond Laser Photolysis Protein Footprinting to Study EGFR Activation by EGF in Cells

Author:: Zhu Yi; Serra Aida; Guo Tiannan; Park Jung Eun; Zhong Qing; Sze Siu Kwan
Source:: Journal of Proteome Research 2017 v.16 no.6 pp. 2282-2293
ISSN:: 1535-3907
Subject:: Escherichia coli; amino acids; crystal structure; hydroxyl radicals; mammals; mass spectrometry; membrane proteins; peptide mapping; peptides; photolysis; proteome
Abstract:: ... Mass spectrometry-based protein footprinting emerged as a useful technology to understand protein ligand interactions in vitro. We have previously demonstrated the application of footprinting in live E. coli cells. Here, we further optimized an ultrafast laser photolysis hydroxyl radical footprinting method and applied it to study the interaction of EGF and EGFR in live mammalian cells. This metho ...
DOI:: 10.1021/acs.jproteome.7b00154
: https://doi.org/10.1021/acs.jproteome.7b00154

11. Arginine (Di)methylated Human Leukocyte Antigen Class I Peptides Are Favorably Presented by HLA-B*07

Author:: Marino Fabio; Mommen Geert P. M.; Jeko Anita; Meiring Hugo D.; van Gaans-van den Brink Jacqueline A. M.; Scheltema Richard A.; van Els Cécile A. C. M.; Heck Albert J. R.
Source:: Journal of Proteome Research 2017 v.16 no.1 pp. 34-44
ISSN:: 1535-3907
Subject:: B-lymphocytes; HLA antigens; T-lymphocytes; alleles; arginine; humans; immune response; immunotherapy; mass spectrometry; peptides; post-translational modification; proline; proteome; transferases
Abstract:: ... Alterations in protein post-translational modification (PTM) are recognized hallmarks of diseases. These modifications potentially provide a unique source of disease-related human leukocyte antigen (HLA) class I-presented peptides that can elicit specific immune responses. While phosphorylated HLA peptides have already received attention, arginine methylated HLA class I peptide presentation has no ...
DOI:: 10.1021/acs.jproteome.6b00528
: https://doi.org/10.1021/acs.jproteome.6b00528

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

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

13. Brain Membrane Proteome and Phosphoproteome Reveal Molecular Basis Associating with Nursing and Foraging Behaviors of Honeybee Workers

Author:: Han Bin; Fang Yu; Feng Mao; Hu Han; Hao Yue; Ma Chuan; Huo Xinmei; Meng Lifeng; Zhang Xufeng; Wu Fan; Li Jianke
Source:: Journal of Proteome Research 2017 v.16 no.10 pp. 3646-3663
ISSN:: 1535-3907
Subject:: Apis mellifera ligustica; adults; arachidonic acid; brain; carbohydrates; foraging; information processing; larvae; membrane proteins; memory; metabolism; mitogen-activated protein kinase; nerve tissue; nucleosides; pheromones; phosphoproteins; phosphorylation; pollen; polyethism; proteome; royal jelly; smell; social behavior; social insects; taurine; transforming growth factor beta; worker honey bees
Abstract:: ... The brain is a vital organ in regulating complex social behaviors of honeybees including learning and memory. Knowledge of how brain membrane proteins and their phosphorylation underlie the age-related behavioral polyethism is still lacking. A hitherto age-resolved brain membrane proteome and phosphoproteome were reported in adult worker bees from two strains of honeybee (Apis mellifera ligustica) ...
DOI:: 10.1021/acs.jproteome.7b00371
: https://doi.org/10.1021/acs.jproteome.7b00371

14. Candida albicans Modifies the Protein Composition and Size Distribution of THP-1 Macrophage-Derived Extracellular Vesicles

Author:: Reales-Calderón Jose Antonio; Vaz Catarina; Monteoliva Lucía; Molero Gloria; Gil Concha
Source:: Journal of Proteome Research 2017 v.16 no.1 pp. 87-105
ISSN:: 1535-3907
Subject:: Candida albicans; candidiasis; cytoskeleton; immune response; lipids; macrophages; messenger RNA; mitogen-activated protein kinase; monocytes; non-coding RNA; pathogens; protein composition; protein secretion; proteins; proteome; proteomics; tumor necrosis factor-alpha
Abstract:: ... The effectiveness of macrophages in the response to systemic candidiasis is crucial to an effective clearance of the pathogen. The secretion of proteins, mRNAs, noncoding RNAs and lipids through extracellular vesicles (EVs) is one of the mechanisms of communication between immune cells. EVs change their cargo to mediate different responses, and may play a role in the response against infections. T ...
DOI:: 10.1021/acs.jproteome.6b00605
: https://doi.org/10.1021/acs.jproteome.6b00605

15. Characterization of the Extracellular Matrix of Normal and Diseased Tissues Using Proteomics

Author:: Naba Alexandra; Pearce Oliver M. T.; Del Rosario Amanda; Ma Duanduan; Ding Huiming; Rajeeve Vinothini; Cutillas Pedro R.; Balkwill Frances R.; Hynes Richard O.
Source:: Journal of Proteome Research 2017 v.16 no.8 pp. 3083-3091
ISSN:: 1535-3907
Subject:: breast neoplasms; cardiovascular diseases; data collection; epithelial cells; extracellular matrix; fibrosis; mammary glands; mass spectrometry; metastasis; omentum; ovarian neoplasms; peptides; proteins; proteome; proteomics; world wide web
Abstract:: ... The extracellular matrix (ECM) is a complex meshwork of insoluble fibrillar proteins and signaling factors interacting together to provide architectural and instructional cues to the surrounding cells. Alterations in ECM organization or composition and excessive ECM deposition have been observed in diseases such as fibrosis, cardiovascular diseases, and cancer. We provide here optimized protocols ...
DOI:: 10.1021/acs.jproteome.7b00191
: https://doi.org/10.1021/acs.jproteome.7b00191

16. Combined Clinical Phenotype and Lipidomic Analysis Reveals the Impact of Chronic Kidney Disease on Lipid Metabolism

Author:: Chen Hua; Chen Lin; Liu Dan; Chen Dan-Qian; Vaziri Nosratola D.; Yu Xiao-Yong; Zhang Li; Su Wei; Bai Xu; Zhao Ying-Yong
Source:: Journal of Proteome Research 2017 v.16 no.4 pp. 1566-1578
ISSN:: 1535-3907
Subject:: blood lipids; blood serum; cholesterol; creatinine; fatty acid composition; free fatty acids; hyperlipidemia; kidney diseases; lipid metabolism; lipoproteins; palmitic acid; patients; phenotype; protein metabolism; proteome; regression analysis; triacylglycerols
Abstract:: ... Chronic kidney disease (CKD) results in significant dyslipidemia and profound changes in lipid and lipoprotein metabolism. The associated dyslipidemia, in turn, contributes to progression of CKD and its cardiovascular complications. To gain an in-depth insight into the disorders of lipid metabolism in advanced CKD, we applied UPLC-HDMS-based lipidomics to measure serum lipid metabolites in 180 pat ...
DOI:: 10.1021/acs.jproteome.6b00956
: https://doi.org/10.1021/acs.jproteome.6b00956

17. Comfortably Numb and Back: Plasma Metabolomics Reveals Biochemical Adaptations in the Hibernating 13-Lined Ground Squirrel

Author:: D’Alessandro Angelo; Nemkov Travis; Bogren Lori K.; Martin Sandra L.; Hansen Kirk C.
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 958-969
ISSN:: 1535-3907
Subject:: Sciuridae; arginine; biochemical pathways; biological clocks; cystathionine; cysteine; evolutionary adaptation; free fatty acids; hibernation; hydrogen sulfide; ischemia; lysine; mammals; medicine; metabolism; metabolomics; methionine; proteome; succinic acid; toxicity; translation (genetics)
Abstract:: ... Hibernation is an evolutionary adaptation that affords some mammals the ability to exploit the cold to achieve extreme metabolic depression (torpor) while avoiding ischemia/reperfusion or hemorrhagic shock injuries. Hibernators cycle periodically out of torpor, restoring high metabolic activity. If understood at the molecular level, the adaptations underlying torpor-arousal cycles may be leveraged ...
DOI:: 10.1021/acs.jproteome.6b00884
: https://doi.org/10.1021/acs.jproteome.6b00884

18. Comparison of False Discovery Rate Control Strategies for Variant Peptide Identifications in Shotgun Proteogenomics

Author:: Ivanov Mark V.; Lobas Anna A.; Karpov Dmitry S.; Moshkovskii Sergei A.; Gorshkov Mikhail V.
Source:: Journal of Proteome Research 2017 v.16 no.5 pp. 1936-1943
ISSN:: 1535-3907
Subject:: Escherichia coli; data collection; databases; humans; mass spectrometry; mutants; peptides; proteome
Abstract:: ... Proteogenomic studies aiming at identification of variant peptides using customized database searches of mass spectrometry data are facing a dilemma of selecting the most efficient database search strategy: A choice has to be made between using combined or sequential searches against reference (wild-type) and mutant protein databases or directly against the mutant database without the wild-type on ...
DOI:: 10.1021/acs.jproteome.6b01014
: https://doi.org/10.1021/acs.jproteome.6b01014

19. Comprehensive Lipoprotein Characterization Using Lipidomics Analysis of Human Plasma

Author:: Christinat Nicolas; Masoodi Mojgan
Source:: Journal of Proteome Research 2017 v.16 no.8 pp. 2947-2953
ISSN:: 1535-3907
Subject:: cardiovascular diseases; chylomicrons; fractionation; gel electrophoresis; high density lipoprotein; humans; hyperlipidemia; lipid composition; lipid metabolism; liquid-liquid extraction; mass spectrometry; nutrients; polyacrylamide; proteome
Abstract:: ... Lipoproteins are responsible for the transport of lipids and other nutrients in the circulation and therefore play an important role in lipid metabolism and dyslipidemia. They have also been linked to multiple metabolic disorders including cardiovascular disease, and thus understanding their lipid composition is of crucial importance. Characterization of lipoproteins is a challenging task due to t ...
DOI:: 10.1021/acs.jproteome.7b00236
: https://doi.org/10.1021/acs.jproteome.7b00236

20. Comprehensive Metabolomic and Lipidomic Profiling of Human Kidney Tissue: A Platform Comparison

Author:: Leuthold Patrick; Schaeffeler Elke; Winter Stefan; Büttner Florian; Hofmann Ute; Mürdter Thomas E.; Rausch Steffen; Sonntag Denise; Wahrheit Judith; Fend Falko; Hennenlotter Jörg; Bedke Jens; Schwab Matthias; Haag Mathias
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 933-944
ISSN:: 1535-3907
Subject:: correlation; humans; hydrophilic interaction chromatography; kidney neoplasms; kidneys; lipids; metabolites; metabolomics; physicochemical properties; proteome; swine
Abstract:: ... Metabolite profiling of tissue samples is a promising approach for the characterization of cancer pathways and tumor classification based on metabolic features. Here, we present an analytical method for nontargeted metabolomics of kidney tissue. Capitalizing on different chemical properties of metabolites allowed us to extract a broad range of molecules covering small polar molecules and less pola ...
DOI:: 10.1021/acs.jproteome.6b00875
: https://doi.org/10.1021/acs.jproteome.6b00875

21. Comprehensive Metabolomics Study To Assess Longitudinal Biochemical Changes and Potential Early Biomarkers in Nonobese Diabetic Mice That Progress to Diabetes

Author:: Buchwald Peter; Tamayo-Garcia Alejandro; Ramamoorthy Sivapriya; Garcia-Contreras Marta; Mendez Armando J.; Ricordi Camillo
Source:: Journal of Proteome Research 2017 v.16 no.10 pp. 3873-3890
ISSN:: 1535-3907
Subject:: 3-hydroxybutyric acid; amino acids; animal disease models; arabinose; biochemical pathways; biomarkers; blood; feces; females; galactitol; hyperglycemia; insulin-dependent diabetes mellitus; males; maltose; metabolites; metabolomics; mice; phosphatidylcholines; proteome; ribose; serotonin
Abstract:: ... A global nontargeted longitudinal metabolomics study was carried out in male and female NOD mice to characterize the time-profile of the changes in the metabolic signature caused by onset of type 1 diabetes (T1D) and identify possible early biomarkers in T1D progressors. Metabolomics profiling of samples collected at five different time-points identified 676 and 706 biochemicals in blood and feces ...
DOI:: 10.1021/acs.jproteome.7b00512
: https://doi.org/10.1021/acs.jproteome.7b00512

22. Comprehensive Proteomics Analysis Reveals Metabolic Reprogramming of Tumor-Associated Macrophages Stimulated by the Tumor Microenvironment

Author:: Liu Di; Chang Cheng; Lu Ning; Wang Xing; Lu Qian; Ren Xiaojie; Ren Peng; Zhao Dianyuan; Wang Lijing; Zhu Yunping; He Fuchu; Tang Li
Source:: Journal of Proteome Research 2017 v.16 no.1 pp. 288-297
ISSN:: 1535-3907
Subject:: animal models; breast neoplasms; cell lines; glycolysis; humans; macrophages; patients; protein synthesis; proteins; proteome; proteomics; signal transduction
Abstract:: ... Tumor-associated macrophages (TAMs) are major components of the tumor microenvironment. Although a role for TAMs in promoting tumor progression has been revealed, the differentiation mechanisms and intrinsic signals of TAMs regulated by the tumor microenvironment remain unclear. Here we constructed an in vitro TAMs cell model, TES-TAMs, which is from tumor-extract-stimulated bone-marrow-derived ma ...
DOI:: 10.1021/acs.jproteome.6b00604
: https://doi.org/10.1021/acs.jproteome.6b00604

23. Cyclophilin B Deficiency Causes Abnormal Dentin Collagen Matrix

Author:: Terajima Masahiko; Taga Yuki; Cabral Wayne A.; Nagasawa Masako; Sumida Noriko; Hattori Shunji; Marini Joan C.; Yamauchi Mitsuo
Source:: Journal of Proteome Research 2017 v.16 no.8 pp. 2914-2923
ISSN:: 1535-3907
Subject:: bone formation; collagen; crosslinking; cyclophilins; glycosylation; heterozygosity; histology; hydroxylation; hydroxylysine; lysine; mass spectrometry; mice; models; phenotype; proteome; tissues
Abstract:: ... Cyclophilin B (CypB) is an endoplasmic reticulum-resident protein that regulates collagen folding, and also contributes to prolyl 3-hydroxylation (P3H) and lysine (Lys) hydroxylation of collagen. In this study, we characterized dentin type I collagen in CypB null (KO) mice, a model of recessive osteogenesis imperfecta type IX, and compared to those of wild-type (WT) and heterozygous (Het) mice. Ma ...
DOI:: 10.1021/acs.jproteome.7b00190
: https://doi.org/10.1021/acs.jproteome.7b00190

24. Decoding the Effect of Isobaric Substitutions on Identifying Missing Proteins and Variant Peptides in Human Proteome

Author:: Choong Wai-Kok; Lih Tung-Shing Mamie; Chen Yu-Ju; Sung Ting-Yi
Source:: Journal of Proteome Research 2017 v.16 no.12 pp. 4415-4424
ISSN:: 1535-3907
Subject:: alternative splicing; amino acids; data collection; humans; peptides; proteins; proteome; proteomics
Abstract:: ... To confirm the existence of missing proteins, we need to identify at least two unique peptides with length of 9–40 amino acids of a missing protein in bottom-up mass-spectrometry-based proteomic experiments. However, an identified unique peptide of the missing protein, even identified with high level of confidence, could possibly coincide with a peptide of a commonly observed protein due to isobar ...
DOI:: 10.1021/acs.jproteome.7b00342
: https://doi.org/10.1021/acs.jproteome.7b00342

25. Differences between Platelets Derived from Neonatal Cord Blood and Adult Peripheral Blood Assessed by Mass Spectrometry

Author:: Stokhuijzen Eva; Koornneef Johanna Maria; Nota Benjamin; van den Eshof Bart Laurens; van Alphen Floris Pieter Joachim; van den Biggelaar Maartje; van der Zwaan Carmen; Kuijk Carlijn; Mertens Koen; Fijnvandraat Karin; Meijer Alexander Benjamin
Source:: Journal of Proteome Research 2017 v.16 no.10 pp. 3567-3575
ISSN:: 1535-3907
Subject:: adults; agonists; blood platelets; collagen; energy; energy metabolism; gene ontology; glycoproteins; integrins; mass spectrometry; mitochondria; protein synthesis; proteome; proteomics; receptors; thromboxanes; umbilical cord
Abstract:: ... It has been proposed that differences may exist between umbilical cord blood (CB) platelets and adult peripheral blood (APB) platelets, including altered protein levels of the main platelet integrins. We have now compared the protein expression profiles of CB and APB platelets employing a label-free comparative proteomics approach. Aggregation studies showed that CB platelets effectively aggregate ...
DOI:: 10.1021/acs.jproteome.7b00298
: https://doi.org/10.1021/acs.jproteome.7b00298

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

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

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

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

28. Evaluating the Characteristics of Reporter Ion Signal Acquired in the Orbitrap Analyzer for Isobaric Mass Tag Proteome Quantification Experiments

Author:: Hughes Christopher S.; Zhu Chenchen; Spicer Victor; Krokhin Oleg V.; Morin Gregg B.
Source:: Journal of Proteome Research 2017 v.16 no.5 pp. 1831-1838
ISSN:: 1535-3907
Subject:: guidelines; peptides; proteome; spectrometers
Abstract:: ... Multiplexed quantification with isobaric chemical tags (e.g., TMT, iTRAQ) provides a robust and efficient means to comparatively examine proteome dynamics between several biological states using a mass spectrometer (MS). The quantitative nature of isobaric tags necessitates strict validation of the observed ion signals in the chosen MS detector before differential patterns are extracted between bi ...
DOI:: 10.1021/acs.jproteome.7b00092
: https://doi.org/10.1021/acs.jproteome.7b00092

29. Evaluation of FASP, SP3, and iST Protocols for Proteomic Sample Preparation in the Low Microgram Range

Author:: Sielaff Malte; Kuharev Jörg; Bohn Toszka; Hahlbrock Jennifer; Bopp Tobias; Tenzer Stefan; Distler Ute
Source:: Journal of Proteome Research 2017 v.16 no.11 pp. 4060-4072
ISSN:: 1535-3907
Subject:: human cell lines; macrophages; models; peptides; phenotype; protein content; proteins; proteome; proteomics
Abstract:: ... Efficient and reproducible sample preparation is a prerequisite for any robust and sensitive quantitative bottom-up proteomics workflow. Here, we performed an independent comparison between single-pot solid-phase-enhanced sample preparation (SP3), filter-aided sample preparation (FASP), and a commercial kit based on the in-StageTip (iST) method. We assessed their performance for the processing of ...
DOI:: 10.1021/acs.jproteome.7b00433
: https://doi.org/10.1021/acs.jproteome.7b00433

30. Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity

Author:: Yu Fengchao; Li Ning; Yu Weichuan
Source:: Journal of Proteome Research 2017 v.16 no.10 pp. 3942-3952
ISSN:: 1535-3907
Subject:: crosslinking; data collection; databases; ions; mass spectrometry; peptides; protein-protein interactions; proteins; proteome
Abstract:: ... Chemical cross-linking coupled to mass spectrometry is a powerful tool to study protein–protein interactions and protein conformations. Two linked peptides are ionized and fragmented to produce a tandem mass spectrum. In such an experiment, a tandem mass spectrum contains ions from two peptides. The peptide identification problem becomes a peptide–peptide pair identification problem. Currently, mo ...
DOI:: 10.1021/acs.jproteome.7b00338
: https://doi.org/10.1021/acs.jproteome.7b00338

31. Experimental Design in Clinical ‘Omics Biomarker Discovery

Author:: Forshed Jenny
Source:: Journal of Proteome Research 2017 v.16 no.11 pp. 3954-3960
ISSN:: 1535-3907
Subject:: biomarkers; experimental design; proteome; statistical analysis; translation (genetics)
Abstract:: ... This tutorial highlights some issues in the experimental design of clinical ‘omics biomarker discovery, how to avoid bias and get as true quantities as possible from biochemical analyses, and how to select samples to improve the chance of answering the clinical question at issue. This includes the importance of defining clinical aim and end point, knowing the variability in the results, randomizat ...
DOI:: 10.1021/acs.jproteome.7b00418
: https://doi.org/10.1021/acs.jproteome.7b00418

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

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

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

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

34. Global Profiling of Metabolite and Lipid Soluble Microbial Products in Anaerobic Wastewater Reactor Supernatant Using UPLC–MSE

Author:: Tipthara Phornpimon; Kunacheva Chinagarn; Soh Yan Ni Annie; Wong Stephen C. C.; Pin Ng Sean; Stuckey David C.; Boehm Bernhard O.
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 559-570
ISSN:: 1535-3907
Subject:: biological production; cardiolipins; ceramides; colloids; gas chromatography-mass spectrometry; membrane bioreactors; metabolism; metabolites; mixed culture; mutagens; proteome; toxicity; ultra-performance liquid chromatography; wastewater; water supply
Abstract:: ... Identification of soluble microbial products (SMPs) released during bacterial metabolism in mixed cultures in bioreactors is essential to understanding fundamental mechanisms of their biological production. SMPs constitute one of the main foulants (together with colloids and bacterial flocs) in membrane bioreactors widely used to treat and ultimately recycle wastewater. More importantly, the compo ...
DOI:: 10.1021/acs.jproteome.6b00681
: https://doi.org/10.1021/acs.jproteome.6b00681

35. Glycosylation Changes Triggered by the Differentiation of Monocytic THP-1 Cell Line into Macrophages

Author:: Delannoy Clément P.; Rombouts Yoann; Groux-Degroote Sophie; Holst Stephanie; Coddeville Bernadette; Harduin-Lepers Anne; Wuhrer Manfred; Elass-Rochard Elisabeth; Guérardel Yann
Source:: Journal of Proteome Research 2017 v.16 no.1 pp. 156-169
ISSN:: 1535-3907
Subject:: antibodies; cell lines; flow cytometry; gangliosides; glycosylation; glycosyltransferases; humans; lectins; macrophages; mass spectrometry; models; neoplasm cells; polysaccharides; proteome; quantitative polymerase chain reaction; sialidase
Abstract:: ... The human acute monocytic leukemia cell line THP-1 is widely used as an in vitro phagocytic cell model because it exhibits several immune properties similar to native monocyte-derived macrophages. In this study, we investigated the alteration of N- and O-linked glycans as well as glycosphingolipids, during THP-1 differentiation, combining mass spectrometry, flow cytometry, and quantitative real-ti ...
DOI:: 10.1021/acs.jproteome.6b00161
: https://doi.org/10.1021/acs.jproteome.6b00161

36. Glycosylation Changes in Serum Proteins Identify Patients with Pancreatic Cancer

Author:: Drabik Anna; Bodzon-Kulakowska Anna; Suder Piotr; Silberring Jerzy; Kulig Jan; Sierzega Marek
Source:: Journal of Proteome Research 2017 v.16 no.4 pp. 1436-1444
ISSN:: 1535-3907
Subject:: amino acid sequences; biomarkers; blood proteins; diagnostic techniques; epitopes; genomics; glycosylation; host-pathogen relationships; immune response; inflammation; pancreatic neoplasms; patients; protein folding; proteome; proteomics
Abstract:: ... After more than a decade of biomarker discovery using advanced proteomic and genomic approaches, very few biomarkers have been involved in clinical diagnostics. Most candidate biomarkers are focused on the protein component. Targeting post-translational modifications (PTMs) in combination with protein sequences will provide superior diagnostic information with regards to sensitivity and specificit ...
DOI:: 10.1021/acs.jproteome.6b00775
: https://doi.org/10.1021/acs.jproteome.6b00775

37. Hydrophobic Interaction Chromatography for Bottom-Up Proteomics Analysis of Single Proteins and Protein Complexes

Author:: Rackiewicz Michal; Große-Hovest Ludger; Alpert Andrew J.; Zarei Mostafa; Dengjel Jörn
Source:: Journal of Proteome Research 2017 v.16 no.6 pp. 2318-2323
ISSN:: 1535-3907
Subject:: antibodies; bioactive properties; humans; hydrophobic interaction chromatography; hydrophobicity; peptide mapping; post-translational modification; proteins; proteome; proteomics; spectroscopy
Abstract:: ... Hydrophobic interaction chromatography (HIC) is a robust standard analytical method to purify proteins while preserving their biological activity. It is widely used to study post-translational modifications of proteins and drug–protein interactions. In the current manuscript we employed HIC to separate proteins, followed by bottom-up LC–MS/MS experiments. We used this approach to fractionate antib ...
DOI:: 10.1021/acs.jproteome.7b00015
: https://doi.org/10.1021/acs.jproteome.7b00015

38. IL- 6 Linkage to Exercise-Induced Shifts in Lipid-Related Metabolites: A Metabolomics-Based Analysis

Author:: Nieman David C.; Sha Wei; Pappan Kirk L.
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 970-977
ISSN:: 1535-3907
Subject:: adipose tissue; beta oxidation; bioinformatics; biopsy; blood sampling; carnitine; cortisol; dicarboxylic acids; epinephrine; equations; exercise; exercise equipment; glycogen; interleukin-6; interleukin-8; ketone bodies; lipolysis; males; medium chain fatty acids; metabolomics; models; muscles; proteome
Abstract:: ... Metabolomics profiling and bioinformatics technologies were used to determine the relationship between exercise-induced increases in IL-6 and lipid-related metabolites. Twenty-four male runners (age 36.5 ± 1.8 y) ran on treadmills to exhaustion (2.26 ± 0.01 h, 24.9 ± 1.3 km, 69.7 ± 1.9% VO₂ₘₐₓ). Vastus lateralis muscle biopsy and blood samples were collected before and immediately after running an ...
DOI:: 10.1021/acs.jproteome.6b00892
: https://doi.org/10.1021/acs.jproteome.6b00892

39. Identification and Validation of Human Missing Proteins and Peptides in Public Proteome Databases: Data Mining Strategy

Author:: Elguoshy Amr; Hirao Yoshitoshi; Xu Bo; Saito Suguru; Quadery Ali F.; Yamamoto Keiko; Mitsui Toshiaki; Yamamoto Tadashi
Source:: Journal of Proteome Research 2017 v.16 no.12 pp. 4403-4414
ISSN:: 1535-3907
Subject:: RNA; databases; humans; olfactory receptors; peptides; proteins; proteome; proteomics; tissues; transcriptomics
Abstract:: ... In an attempt to complete human proteome project (HPP), Chromosome-Centric Human Proteome Project (C-HPP) launched the journey of missing protein (MP) investigation in 2012. However, 2579 and 572 protein entries in the neXtProt (2017-1) are still considered as missing and uncertain proteins, respectively. Thus, in this study, we proposed a pipeline to analyze, identify, and validate human missing ...
DOI:: 10.1021/acs.jproteome.7b00423
: https://doi.org/10.1021/acs.jproteome.7b00423

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

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

41. Identification of Genes Associated with Breast Cancer Metastasis to Bone on a Protein–Protein Interaction Network with a Shortest Path Algorithm

Author:: Cai Yu-Dong; Zhang Qing; Zhang Yu-Hang; Chen Lei; Huang Tao
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 1027-1038
ISSN:: 1535-3907
Subject:: algorithms; breast neoplasms; breasts; carcinogenesis; genes; humans; metastasis; neoplasm cells; protein-protein interactions; proteome
Abstract:: ... Tumor metastasis is defined as the spread of tumor cells from one organ or part to another that is not directly connected to it, which significantly contributes to the progression and aggravation of tumorigenesis. Because it always involves multiple organs, the metastatic process is difficult to study in its entirety. Complete identification of the genes related to this process is an alternative w ...
DOI:: 10.1021/acs.jproteome.6b00950
: https://doi.org/10.1021/acs.jproteome.6b00950

42. Identification of Novel Protein Expression Changes Following Cisplatin Treatment and Application to Combination Therapy

Author:: Stark Amy L.; Madian Ashraf G.; Williams Sawyer W.; Chen Vincent; Wing Claudia; Hause Ronald J.; To Lida Anita; Gill Amy L.; Myers Jamie L.; Gorsic Lidija K.; Ciaccio Mark F.; White Kevin P.; Jones Richard B.; Dolan M. Eileen
Source:: Journal of Proteome Research 2017 v.16 no.11 pp. 4227-4236
ISSN:: 1535-3907
Subject:: cell lines; cisplatin; drug therapy; head; lung neoplasms; lungs; neck; protein synthesis; proteome; testes; transcription factors
Abstract:: ... Determining the effect of chemotherapeutic treatment on changes in protein expression can provide important targets for overcoming resistance. Due to challenges in simultaneously measuring large numbers of proteins, a paucity of data exists on global changes. To overcome these challenges, we utilized microwestern arrays that allowed us to measure the abundance and modification state of hundreds of ...
DOI:: 10.1021/acs.jproteome.7b00576
: https://doi.org/10.1021/acs.jproteome.7b00576

43. Identification of Urinary Food Intake Biomarkers for Milk, Cheese, and Soy-Based Drink by Untargeted GC-MS and NMR in Healthy Humans

Author:: Münger Linda H.; Trimigno Alessia; Picone Gianfranco; Freiburghaus Carola; Pimentel Grégory; Burton Kathryn J.; Pralong François P.; Vionnet Nathalie; Capozzi Francesco; Badertscher René; Vergères Guy
Source:: Journal of Proteome Research 2017 v.16 no.9 pp. 3321-3335
ISSN:: 1535-3907
Subject:: alanine; allantoin; biomarkers; cheeses; cross-over studies; females; galactitol; galactose; gas chromatography-mass spectrometry; humans; lactose; males; metabolites; milk; milk consumption; nuclear magnetic resonance spectroscopy; nutrition assessment; pinitol; proline; proteome; soybean products; trigonelline; urine
Abstract:: ... The measurement of food intake biomarkers (FIBs) in biofluids represents an objective tool for dietary assessment. FIBs of milk and cheese still need more investigation due to the absence of candidate markers. Thus, an acute intervention study has been performed to sensitively and specifically identify candidate FIBs. Eleven healthy male and female volunteers participated in the randomized, contro ...
DOI:: 10.1021/acs.jproteome.7b00319
: https://doi.org/10.1021/acs.jproteome.7b00319

44. Identifications of Putative PKA Substrates with Quantitative Phosphoproteomics and Primary-Sequence-Based Scoring

Author:: Imamura Haruna; Wagih Omar; Niinae Tomoya; Sugiyama Naoyuki; Beltrao Pedro; Ishihama Yasushi
Source:: Journal of Proteome Research 2017 v.16 no.4 pp. 1825-1830
ISSN:: 1535-3907
Subject:: apoptosis; cAMP-dependent protein kinase; drugs; humans; models; phosphopeptides; phosphorylation; proteome; proteomics; serine; threonine
Abstract:: ... Protein kinase A (PKA or cAMP-dependent protein kinase) is a serine/threonine kinase that plays essential roles in the regulation of proliferation, differentiation, and apoptosis. To better understand the functions of PKA, it is necessary to elucidate the direct interplay between PKA and their substrates in living human cells. To identify kinase target substrates in a high-throughput manner, we fi ...
DOI:: 10.1021/acs.jproteome.7b00087
: https://doi.org/10.1021/acs.jproteome.7b00087

45. Immuno-affinity Capture Followed by TMPP N-Terminus Tagging to Study Catabolism of Therapeutic Proteins

Author:: Kullolli Majlinda; Rock Dan A.; Ma Ji
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 911-919
ISSN:: 1535-3907
Subject:: biopharmaceuticals; blood serum; desorption; digestion; electrospray ionization mass spectrometry; humans; hydrophobicity; ionization; liquids; metabolites; mice; peptides; pharmacodynamics; pharmacokinetics; protein engineering; proteins; proteolysis; proteome
Abstract:: ... Characterization of in vitro and in vivo catabolism of therapeutic proteins has increasingly become an integral part of discovery and development process for novel proteins. Unambiguous and efficient identification of catabolites can not only facilitate accurate understanding of pharmacokinetic profiles of drug candidates, but also enables follow up protein engineering to generate more catabolical ...
DOI:: 10.1021/acs.jproteome.6b00863
: https://doi.org/10.1021/acs.jproteome.6b00863

46. Impact of the Niemann–Pick c1 Gene Mutation on the Total Cellular Glycomics of CHO Cells

Author:: Furukawa Jun-ichi; Soga Minami; Okada Kazue; Yokota Ikuko; Piao Jinhua; Irie Tetsumi; Era Takumi; Shinohara Yasuro
Source:: Journal of Proteome Research 2017 v.16 no.8 pp. 2802-2810
ISSN:: 1535-3907
Subject:: Chinese hamsters; animal ovaries; cholesterol; genes; glycomics; glycosphingolipids; mutants; mutation; oligosaccharides; proteome
Abstract:: ... Niemann–Pick disease type C (NPC) is an autosomal recessive lipid storage disorder, and the majority of cases are caused by mutations in the NPC1 gene. In this study, we clarified how a single gene mutation in the NPC1 gene impacts the cellular glycome by analyzing the total glycomic expression profile of Chinese hamster ovary cell mutants defective in the Npc1 gene (Npc1 KO CHO cells). A number o ...
DOI:: 10.1021/acs.jproteome.7b00070
: https://doi.org/10.1021/acs.jproteome.7b00070

47. Impact of the Pd2Spermine Chelate on Osteosarcoma Metabolism: An NMR Metabolomics Study

Author:: Lamego Inês; Marques M. Paula M.; Duarte Iola F.; Martins Ana S.; Oliveira Helena; Gil Ana M.
Source:: Journal of Proteome Research 2017 v.16 no.4 pp. 1773-1783
ISSN:: 1535-3907
Subject:: amino acid metabolism; apoptosis; biosynthesis; choline; cisplatin; cytotoxicity; doxorubicin; glutathione; glycosylation; hypoxanthine; inositols; lipid metabolism; lipids; metabolomics; methionine; methotrexate; nuclear magnetic resonance spectroscopy; osteosarcoma; palladium; proteome; serine; uridine diphosphate
Abstract:: ... A metabolomics study of Pd₂Spermine(Spm) on osteosarcoma MG-63 and osteoblastic HOb cells is presented to assess the impact of the potential palladium drug on cell metabolism compared with cisplatin (cDDP). Despite its higher cytotoxicity, Pd₂Spm induced lower (and reversible) metabolic impact on MG-63 cells and the absence of apoptosis; conversely, it induced significant deviations in osteoblasti ...
DOI:: 10.1021/acs.jproteome.7b00035
: https://doi.org/10.1021/acs.jproteome.7b00035

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

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

49. Improvements in Mass Spectrometry Assay Library Generation for Targeted Proteomics

Author:: Teleman Johan; Hauri Simon; Malmström Johan
Source:: Journal of Proteome Research 2017 v.16 no.7 pp. 2384-2392
ISSN:: 1535-3907
Subject:: algorithms; mass spectrometry; mice; proteins; proteome; proteomics
Abstract:: ... In data-independent acquisition mass spectrometry (DIA-MS), targeted extraction of peptide signals in silico using mass spectrometry assay libraries is a successful method for the identification and quantification of proteins. However, it remains unclear if high quality assay libraries with more accurate peptide ion coordinates can improve peptide target identification rates in DIA analysis. In th ...
DOI:: 10.1021/acs.jproteome.6b00928
: https://doi.org/10.1021/acs.jproteome.6b00928

50. In Situ Characterization of Tissue-Resident Immune Cells by MALDI Mass Spectrometry Imaging

Author:: Holzlechner Matthias; Strasser Katharina; Zareva Elitsa; Steinhäuser Luise; Birnleitner Hanna; Beer Andrea; Bergmann Michael; Oehler Rudolf; Marchetti-Deschmann Martina
Source:: Journal of Proteome Research 2017 v.16 no.1 pp. 65-76
ISSN:: 1535-3907
Subject:: T-lymphocytes; colon; humans; image analysis; macrophages; matrix-assisted laser desorption-ionization mass spectrometry; monocytes; mucosa; patients; phenotype; proteome
Abstract:: ... Tissue-resident immune cells differ from their corresponding blood cells in many functional aspects. Although the proteome of blood immune cells has been well-investigated, there are almost no data on tissue-resident immune cells. Here, we explored the potential of using MALDI-TOF-MS imaging (MSI) to investigate these cells in colon tissue, which exhibits a strong infiltration of immune cells. MSI ...
DOI:: 10.1021/acs.jproteome.6b00610
: https://doi.org/10.1021/acs.jproteome.6b00610

51. Infections with the Sexually Transmitted Pathogen Nosema apis Trigger an Immune Response in the Seminal Fluid of Honey Bees (Apis mellifera)

Author:: Grassl Julia; Peng Yan; Baer-Imhoof Barbara; Welch Mat; Millar A. Harvey; Baer Boris
Source:: Journal of Proteome Research 2017 v.16 no.1 pp. 319-334
ISSN:: 1535-3907
Subject:: Apis mellifera; Nosema apis; antifungal properties; chitinase; fungi; honey bees; immune response; isotope labeling; males; parasites; pathogens; proteome; risk; seminal plasma proteins
Abstract:: ... Honey bee (Apis mellifera) males are highly susceptible to infections with the sexually transmitted fungal pathogen Nosema apis. However, they are able to suppress this parasite in the ejaculate using immune molecules in the seminal fluid. We predicted that males respond to infections by altering the seminal fluid proteome to minimize the risk to sexually transmit the parasite to the queen and her ...
DOI:: 10.1021/acs.jproteome.6b00051
: https://doi.org/10.1021/acs.jproteome.6b00051

52. Influence of Ingesting a Flavonoid-Rich Supplement on the Metabolome and Concentration of Urine Phenolics in Overweight/Obese Women

Author:: Nieman David C.; Ramamoorthy Sivapriya; Kay Colin D.; Goodman Courtney L.; Capps Christopher R.; Shue Zack L.; Heyl Nicole; Grace Mary H.; Lila Mary A.
Source:: Journal of Proteome Research 2017 v.16 no.8 pp. 2924-2935
ISSN:: 1535-3907
Subject:: adults; ascorbic acid; bilberries; blood; body mass index; caffeine; clinical trials; females; fruit extracts; green tea; inflammation; ingestion; interleukin-6; leaf extracts; metabolites; metabolome; metabolomics; obesity; omega-3 fatty acids; oxidative stress; phenolic compounds; propionic acid; proteome; quercetin; sulfates; urine; women; xenobiotics
Abstract:: ... This study evaluated the effect of ingesting a flavonoid-rich supplement (329 mg/d) on total urine phenolics and shifts in plasma metabolites in overweight/obese female adults using untargeted metabolomics procedures. Participants (N = 103, 18–65 y, BMI ≥ 25 kg/m²) were randomized to flavonoid (F) or placebo (P) groups for 12 weeks with blood and 24 h urine samples collected prestudy and after 4 a ...
DOI:: 10.1021/acs.jproteome.7b00196
: https://doi.org/10.1021/acs.jproteome.7b00196

53. Integrative Analysis of Renal Ischemia/Reperfusion Injury and Remote Ischemic Preconditioning in Mice

Author:: Cho Kumsun; Min Sang-il; Ahn Sanghyun; Min Seung-Kee; Ahn Curie; Yu Kyung-Sang; Jang In-Jin; Cho Joo-Youn; Ha Jongwon
Source:: Journal of Proteome Research 2017 v.16 no.8 pp. 2877-2886
ISSN:: 1535-3907
Subject:: blood serum; humans; ischemia; kidneys; messenger RNA; metabolome; mice; oxidative stress; protective effect; protein synthesis; proteome; urine
Abstract:: ... Remote ischemic preconditioning (RIPC) is a strategy to induce resistance in a target organ against the oxidative stress and injury caused by ischemia and reperfusion (IR). RIPC harnesses the body’s endogenous protective capabilities through brief episodes of IR applied in organs remote from the target. Few studies have analyzed this phenomenon in the kidney. Furthermore, the window of protection ...
DOI:: 10.1021/acs.jproteome.7b00167
: https://doi.org/10.1021/acs.jproteome.7b00167

54. Intra- and Interskeletal Proteome Variations in Fresh and Buried Bones

Author:: Procopio Noemi; Chamberlain Andrew T.; Buckley Michael
Source:: Journal of Proteome Research 2017 v.16 no.5 pp. 2016-2029
ISSN:: 1535-3907
Subject:: archaeology; blood proteins; bones; death; forensic sciences; longevity; paleontology; pig carcasses; postmortem changes; proteome; proteomics
Abstract:: ... Proteomic methods are acquiring greater importance in archaeology and palaeontology due to the longevity of proteins in skeletal remains. There are also developing interests in forensic applications, offering the potential to shed light on post-mortem intervals and age at death estimation. However, our understanding of intra- and interskeletal proteome variations is currently severely limited. Her ...
DOI:: 10.1021/acs.jproteome.6b01070
: https://doi.org/10.1021/acs.jproteome.6b01070

55. Intrinsically Disordered Proteins as Important Players during Desiccation Stress of Soybean Radicles

Author:: Liu Yun; Wu Jiahui; Sun Nan; Tu Chengjian; Shi Xiaoying; Cheng Hua; Liu Simu; Li Shuiming; Wang Yong; Zheng Yizhi; Uversky Vladimir N.
Source:: Journal of Proteome Research 2017 v.16 no.7 pp. 2393-2409
ISSN:: 1535-3907
Subject:: Glycine max; biosynthesis; boiling; cysteine; freeze-thaw cycles; heat stability; lactate dehydrogenase; methionine; proteins; proteome; seedling growth; seeds; soybeans
Abstract:: ... Intrinsically disordered proteins (IDPs) play a variety of important physiological roles in all living organisms. However, there is no comprehensive analysis of the abundance of IDPs associated with environmental stress in plants. Here, we show that a set of heat-stable proteins (i.e., proteins that do not denature after boiling at 100 °C for 10 min) was present in R₀ₘₘ and R₁₅ₘₘ radicles (i.e., b ...
DOI:: 10.1021/acs.jproteome.6b01045
: https://doi.org/10.1021/acs.jproteome.6b01045

56. Large-Scale Identification of Protein Crotonylation Reveals Its Role in Multiple Cellular Functions

Author:: Wei Wei; Mao Anqi; Tang Bin; Zeng Qiufang; Gao Shennan; Lu Lu; Li Wenpeng; Du James X.; Li Jiwen; Wong Jiemin; Liao Lujian
Source:: Journal of Proteome Research 2017 v.16 no.4 pp. 1743-1752
ISSN:: 1535-3907
Subject:: RNA; antibodies; bioinformatics; cell cycle; gene expression; heterochromatin; histones; lysine; mass spectrometry; post-translational modification; proteome; transcription (genetics)
Abstract:: ... Lysine crotonylation on histones is a recently identified post-translational modification that has been demonstrated to associate with active promoters and to directly stimulate transcription. Given that crotonyl-CoA is essential for the acyl transfer reaction and it is a metabolic intermediate widely localized within the cell, we postulate that lysine crotonylation on nonhistone proteins could al ...
DOI:: 10.1021/acs.jproteome.7b00012
: https://doi.org/10.1021/acs.jproteome.7b00012

57. Large-Scale SRM Screen of Urothelial Bladder Cancer Candidate Biomarkers in Urine

Author:: Duriez Elodie; Masselon Christophe D.; Mesmin Cédric; Court Magali; Demeure Kevin; Allory Yves; Malats Núria; Matondo Mariette; Radvanyi François; Garin Jérôme; Domon Bruno
Source:: Journal of Proteome Research 2017 v.16 no.4 pp. 1617-1631
ISSN:: 1535-3907
Subject:: biomarkers; data collection; liquids; monitoring; morbidity; mortality; patient care; patients; peptides; proteins; proteome; proteomics; transcriptomics; urinalysis; urinary bladder neoplasms; urine
Abstract:: ... Urothelial bladder cancer is a condition associated with high recurrence and substantial morbidity and mortality. Noninvasive urinary tests that would detect bladder cancer and tumor recurrence are required to significantly improve patient care. Over the past decade, numerous bladder cancer candidate biomarkers have been identified in the context of extensive proteomics or transcriptomics studies. ...
DOI:: 10.1021/acs.jproteome.6b00979
: https://doi.org/10.1021/acs.jproteome.6b00979

58. Limiting the Hydrolysis and Oxidation of Maleimide–Peptide Adducts Improves Detection of Protein Thiol Oxidation

Author:: Boyatzis Amber E.; Bringans Scott D.; Piggott Matthew J.; Duong Marisa N.; Lipscombe Richard J.; Arthur Peter G.
Source:: Journal of Proteome Research 2017 v.16 no.5 pp. 2004-2015
ISSN:: 1535-3907
Subject:: alkylation; buffers; cysteine; gel electrophoresis; gels; hydrolysis; nitrogen; oxidation; oxidative stress; oxygen; pH; pathophysiology; peptides; proteins; proteolysis; proteome; proteomics; staining; thiols
Abstract:: ... Oxidative stress, caused by reactive oxygen and nitrogen species (RONS), is important in the pathophysiology of many diseases. A key target of RONS is the thiol group of protein cysteine residues. Because thiol oxidation can affect protein function, mechanistic information about how oxidative stress affects tissue function can be ascertained by identifying oxidized proteins. The probes used must b ...
DOI:: 10.1021/acs.jproteome.6b01060
: https://doi.org/10.1021/acs.jproteome.6b01060

59. Lycopene Prevents Mitochondrial Dysfunction during d-Galactosamine/Lipopolysaccharide-Induced Fulminant Hepatic Failure in Albino Rats

Author:: Sheriff Sheik Abdulazeez; Shaik Ibrahim Shaikhussain; Devaki Thiruvengadam; Chakraborty Sandipan; Agarwal Subhash; Pérez-Sánchez Horacio
Source:: Journal of Proteome Research 2017 v.16 no.9 pp. 3190-3199
ISSN:: 1535-3907
Subject:: adenosine triphosphate; albino; antioxidant activity; body weight; electron transport chain; enzyme activity; enzymes; hydrogen peroxide; lipid peroxidation; lipid peroxides; liver; liver failure; lungs; lycopene; mitochondria; mitochondrial membrane; molecular models; neoplasms; oxidative stress; proteome; rats; toxicity; tricarboxylic acid cycle
Abstract:: ... Functional perturbation of mitochondria is associated with fulminant hepatic failure (FHF). d-Galactosamine/lipopolysaccharide (d-GalN/LPS)-induced FHF is a renowned model to evaluate the efficacy of hepatoprotective agents. Lycopene is an antioxidant and phytonutrient from the carotenoid family. The health benefits of lycopene are prominent against cancer and cardiovascular, lung, liver, and skin ...
DOI:: 10.1021/acs.jproteome.7b00176
: https://doi.org/10.1021/acs.jproteome.7b00176

60. MALDI versus ESI: The Impact of the Ion Source on Peptide Identification

Author:: Nadler Wiebke Maria; Waidelich Dietmar; Kerner Alexander; Hanke Sabrina; Berg Regina; Trumpp Andreas; Rösli Christoph
Source:: Journal of Proteome Research 2017 v.16 no.3 pp. 1207-1215
ISSN:: 1535-3907
Subject:: amino acid composition; data collection; desorption; human cell lines; hydrophobicity; ionization; mass spectrometry; peptides; proteome; proteomics; statistical analysis
Abstract:: ... For mass spectrometry-based proteomic analyses, electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) are the commonly used ionization techniques. To investigate the influence of the ion source on peptide detection in large-scale proteomics, an optimized GeLC/MS workflow was developed and applied either with ESI/MS or with MALDI/MS for the proteomic analysis of diff ...
DOI:: 10.1021/acs.jproteome.6b00805
: https://doi.org/10.1021/acs.jproteome.6b00805

61. Malonylome Analysis Reveals the Involvement of Lysine Malonylation in Metabolism and Photosynthesis in Cyanobacteria

Author:: Ma Yanyan; Yang Mingkun; Lin Xiaohuang; Liu Xin; Huang Hui; Ge Feng
Source:: Journal of Proteome Research 2017 v.16 no.5 pp. 2030-2043
ISSN:: 1535-3907
Subject:: Synechocystis sp. PCC 6803; autotrophs; bacteria; bioinformatics; lysine; mammals; models; phosphoglycerate kinase; photosynthesis; post-translational modification; primary productivity; prokaryotic cells; proteins; proteome; proteomics; site-directed mutagenesis; surveys; tandem mass spectrometry
Abstract:: ... As a recently validated reversible post translational modification, lysine malonylation regulates diverse cellular processes from bacteria to mammals, but its existence and function in photosynthetic organisms remain unknown. Cyanobacteria are the most ancient group of photosynthetic prokaryotes and contribute about 50% of the total primary production on Earth. Previously, we reported the lysine a ...
DOI:: 10.1021/acs.jproteome.7b00017
: https://doi.org/10.1021/acs.jproteome.7b00017

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

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

63. Metabolic Pathways Regulated by Chitosan Contributing to Drought Resistance in White Clover

Author:: Li Zhou; Zhang Yan; Zhang Xinquan; Merewitz Emily; Peng Yan; Ma Xiao; Huang Linkai; Yan Yanhong
Source:: Journal of Proteome Research 2017 v.16 no.8 pp. 3039-3052
ISSN:: 1535-3907
Subject:: Trifolium repens; antioxidant activity; carbohydrate metabolism; chitosan; drought tolerance; energy; energy metabolism; flavonoids; gamma-aminobutyric acid; gene expression regulation; genes; glutathione; growth chambers; homeostasis; metabolites; metabolome; phenotype; proteome; putrescine; spermidine; sugar alcohols; transcriptome; tricarboxylic acid cycle
Abstract:: ... Increased endogenous chitosan (CTS) could be associated with improved drought resistance in white clover (Trifolium repens). Plants were pretreated with or without 1 mg/mL CTS and then were subjected to optimal or water-limited condition in controlled growth chambers for 6 days. Phenotypic and physiological results indicated that exogenous CTS significantly improved drought resistance of white clo ...
DOI:: 10.1021/acs.jproteome.7b00334
: https://doi.org/10.1021/acs.jproteome.7b00334

64. Metabolic Phenotype of Obesity in a Saudi Population

Author:: Ahmad Muhammad Saeed; Alsaleh Munirah; Kimhofer Torben; Ahmad Sultan; Jamal Wisam; Wali Siraj Omar; Nicholson Jeremy Kirk; Damanhouri Zoheir Abdullah; Holmes Elaine
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 635-644
ISSN:: 1535-3907
Subject:: bile acids; blood serum; carboxylic acids; cholesterol; comorbidity; enzymes; glycoproteins; high density lipoprotein; intestinal microorganisms; liver function; lysine; metabolites; nuclear magnetic resonance spectroscopy; obesity; phenotype; proteome; risk; sugars; triacylglycerols; tricarboxylic acid cycle; urine; Middle East
Abstract:: ... Metabolic phenotyping of obese populations can shed light on understanding environmental interactions underpinning obesogenesis. Obesity and its comorbidities are a major health and socioeconomic concern globally and are highly prevalent in the Middle East. We employed nuclear magnetic resonance spectroscopy to characterize the metabolic signature of urine and blood plasma for a cohort of obese (n ...
DOI:: 10.1021/acs.jproteome.6b00710
: https://doi.org/10.1021/acs.jproteome.6b00710

65. Metabolic Response to Everolimus in Patient-Derived Triple-Negative Breast Cancer Xenografts

Author:: Euceda Leslie R.; Hill Deborah K.; Stokke Endre; Hatem Rana; El Botty Rania; Bièche Ivan; Marangoni Elisabetta; Bathen Tone F.; Moestue Siver A.
Source:: Journal of Proteome Research 2017 v.16 no.5 pp. 1868-1879
ISSN:: 1535-3907
Subject:: animals; biochemical pathways; biomarkers; breast neoplasms; disease course; drug therapy; drugs; glycolysis; lactic acid; magnetism; metabolites; metabolomics; models; mutation; patients; phosphatidylinositol 3-kinase; prediction; proteome; signal transduction; spectroscopy
Abstract:: ... Patients with triple-negative breast cancer (TNBC) are unresponsive to endocrine and anti-HER2 pharmacotherapy, limiting their therapeutic options to chemotherapy. TNBC is frequently associated with abnormalities in the PI3K/AKT/mTOR signaling pathway; drugs targeting this pathway are currently being evaluated in these patients. However, the response is variable, partly due to heterogeneity within ...
DOI:: 10.1021/acs.jproteome.6b00918
: https://doi.org/10.1021/acs.jproteome.6b00918

66. Metabolomic Fingerprinting in Various Body Fluids of a Diet-Controlled Clinical Smoking Cessation Study Using a Validated GC-TOF-MS Metabolomics Platform

Author:: Goettel Michael; Niessner Reinhard; Mueller Daniel; Scherer Max; Scherer Gerhard; Pluym Nikola
Source:: Journal of Proteome Research 2017 v.16 no.10 pp. 3491-3503
ISSN:: 1535-3907
Subject:: amino acid metabolism; biochemical pathways; body fluids; compliance; cotinine; fatty acids; males; metabolites; metabolomics; proteome; saliva; urine
Abstract:: ... Untargeted GC-TOF-MS analysis proved to be a suitable analytical platform to determine alterations in the metabolic profile. Several metabolic pathways were found to be altered in a first clinical study comparing smokers against nonsmokers. Subsequently, we conducted a clinical diet-controlled study to investigate alterations in the metabolic profile during the course of 3 months of smoking cessat ...
DOI:: 10.1021/acs.jproteome.7b00128
: https://doi.org/10.1021/acs.jproteome.7b00128

67. Metabolomics-Based Elucidation of Active Metabolic Pathways in Erythrocytes and HSC-Derived Reticulocytes

Author:: Srivastava Anubhav; Evans Krystal J.; Sexton Anna E.; Schofield Louis; Creek Darren J.
Source:: Journal of Proteome Research 2017 v.16 no.4 pp. 1492-1505
ISSN:: 1535-3907
Subject:: biosynthesis; databases; glucose; glycolysis; isotope labeling; metabolites; metabolomics; pentose phosphate cycle; proteome; reticulocytes; stable isotopes
Abstract:: ... A detailed analysis of the metabolic state of human-stem-cell-derived erythrocytes allowed us to characterize the existence of active metabolic pathways in younger reticulocytes and compare them to mature erythrocytes. Using high-resolution LC–MS-based untargeted metabolomics, we found that reticulocytes had a comparatively much richer repertoire of metabolites, which spanned a range of metabolite ...
DOI:: 10.1021/acs.jproteome.6b00902
: https://doi.org/10.1021/acs.jproteome.6b00902

68. Minimizing Laboratory-Induced Decay in Bone Proteomics

Author:: Procopio Noemi; Buckley Michael
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 447-458
ISSN:: 1535-3907
Subject:: ammonium acetate; asparagine; deamidation; forensic sciences; glutamine; guanidines; phylogeny; post-translational modification; proteins; proteome; proteomics; species identification
Abstract:: ... Proteomics methods are being increasingly used to study archaeological and palaeontological bone, assisting in species identification and phylogenetic studies as well as improving our understanding of bone diagenesis. More recently, there are developing interests in the study of post-translational modifications, some of which are potentially diagnostic of decay, but none of the previous extraction ...
DOI:: 10.1021/acs.jproteome.6b00564
: https://doi.org/10.1021/acs.jproteome.6b00564

69. Model for Quality Control of Allergen Products with Mass Spectrometry

Author:: Spiric Jelena; Schulenborg Thomas; Schwaben Luisa; Engin Anna M.; Karas Michael; Reuter Andreas
Source:: Journal of Proteome Research 2017 v.16 no.10 pp. 3852-3862
ISSN:: 1535-3907
Subject:: Betula; allergens; hay fever; mass spectrometry; models; monitoring; pollen; protein composition; proteins; proteome; quality control
Abstract:: ... Birch pollen allergy is diagnosed and treated with aqueous extracts from birch pollen, which contain a mixture of allergens and nonallergenic proteins, including large numbers of closely related sequence variants, so-called iso-allergens of the major allergen, Bet v 1. The quality of therapeutic and diagnostic allergen products largely depends on the allergen and iso-allergen composition. Several ...
DOI:: 10.1021/acs.jproteome.7b00490
: https://doi.org/10.1021/acs.jproteome.7b00490

70. Molecular Dynamics Information Improves cis-Peptide-Based Function Annotation of Proteins

Author:: Das Sreetama; Bhadra Pratiti; Ramakumar Suryanarayanarao; Pal Debnath
Source:: Journal of Proteome Research 2017 v.16 no.8 pp. 2936-2946
ISSN:: 1535-3907
Subject:: cis-trans isomerism; cis-trans isomers; molecular dynamics; prediction; proteins; proteome
Abstract:: ... cis-Peptide bonds, whose occurrence in proteins is rare but evolutionarily conserved, are implicated to play an important role in protein function. This has led to their previous use in a homology-independent, fragment-match-based protein function annotation method. However, proteins are not static molecules; dynamics is integral to their activity. This is nicely epitomized by the geometric isomer ...
DOI:: 10.1021/acs.jproteome.7b00217
: https://doi.org/10.1021/acs.jproteome.7b00217

71. Multiplexed MRM-Based Protein Quantitation Using Two Different Stable Isotope-Labeled Peptide Isotopologues for Calibration

Author:: LeBlanc André; Michaud Sarah A.; Percy Andrew J.; Hardie Darryl B.; Yang Juncong; Sinclair Nicholas J.; Proudfoot Jillaine I.; Pistawka Adam; Smith Derek S.; Borchers Christoph H.
Source:: Journal of Proteome Research 2017 v.16 no.7 pp. 2527-2536
ISSN:: 1535-3907
Subject:: biomedical research; blood proteins; humans; mass spectrometry; peptides; proteome; quality control
Abstract:: ... When quantifying endogenous plasma proteins for fundamental and biomedical research − as well as for clinical applications − precise, reproducible, and robust assays are required. Targeted detection of peptides in a bottom-up strategy is the most common and precise mass spectrometry-based quantitation approach when combined with the use of stable isotope-labeled peptides. However, when measuring p ...
DOI:: 10.1021/acs.jproteome.7b00094
: https://doi.org/10.1021/acs.jproteome.7b00094

72. Placental Proteomics Provides Insights into Pathophysiology of Pre-Eclampsia and Predicts Possible Markers in Plasma

Author:: Mary Sheon; Kulkarni Mahesh J.; Malakar Dipankar; Joshi Sadhana R.; Mehendale Savita S.; Giri Ashok P.
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 1050-1060
ISSN:: 1535-3907
Subject:: angiogenesis; apolipoproteins; apoptosis; biomarkers; gene expression regulation; gene ontology; haptoglobins; hypertension; hypoxia; monitoring; oxidative stress; pathogenesis; pathophysiology; patients; placenta; pre-eclampsia; pregnancy; protein synthesis; proteinuria; proteome; proteomics
Abstract:: ... Pre-eclampsia is a hypertensive disorder characterized by the new onset of hypertension >140/90 mmHg and proteinuria after the 20th week of gestation. The disorder is multifactorial and originates with abnormal placentation. Comparison of the placental proteome of normotensive (n = 25) and pre-eclamptic (n = 25) patients by gel-free proteomic techniques identified a total of 2145 proteins in the p ...
DOI:: 10.1021/acs.jproteome.6b00955
: https://doi.org/10.1021/acs.jproteome.6b00955

73. Primary Metabolism and Medium-Chain Fatty Acid Alterations Precede Long-Chain Fatty Acid Changes Impacting Neutral Lipid Metabolism in Response to an Anticancer Lysophosphatidylcholine Analogue in Yeast

Author:: Tambellini Nicolas P.; Zaremberg Vanina; Krishnaiah Saikumari; Turner Raymond J.; Weljie Aalim M.
Source:: Journal of Proteome Research 2017 v.16 no.10 pp. 3741-3752
ISSN:: 1535-3907
Subject:: alanine; cell death; citrates; diacylglycerols; drug therapy; fatty acid composition; gamma-aminobutyric acid; growth retardation; homeostasis; inositols; lipid metabolism; lysophosphatidylcholine; mass spectrometry; metabolites; metabolomics; mitochondria; oxidative stress; proline; proteome; prototypes; trehalose; tricarboxylic acid cycle; very long chain fatty acids; yeasts
Abstract:: ... The nonmetabolizable lysophosphatidylcholine (LysoPC) analogue edelfosine is the prototype of a class of compounds being investigated for their potential as selective chemotherapeutic agents. Edelfosine targets membranes, disturbing cellular homeostasis. Is not clear at this point how membrane alterations are communicated between intracellular compartments leading to growth inhibition and eventual ...
DOI:: 10.1021/acs.jproteome.7b00430
: https://doi.org/10.1021/acs.jproteome.7b00430

74. Progress and Future Direction of Chromosome-Centric Human Proteome Project

Author:: Paik Young-Ki; Overall Christopher M.; Deutsch Eric W.; Van Eyk Jennifer E.; Omenn Gilbert S.
Source:: Journal of Proteome Research 2017 v.16 no.12 pp. 4253-4258
ISSN:: 1535-3907
Subject:: analytical methods; guidelines; humans; proteins; proteome; teams
Abstract:: ... This special issue of JPR celebrates the fifth anniversary of the Chromosome-Centric Human Proteome Project (C-HPP). We present 27 manuscripts in four categories: (i) Metrics of Progress and Resources, (ii) Missing Protein Detection and Validation, (iii) Analytical Methods and Quality Assessment, and (iv) Protein Functions and Disease. We briefly introduce key messages from each paper, mostly from ...
DOI:: 10.1021/acs.jproteome.7b00734
: https://doi.org/10.1021/acs.jproteome.7b00734

75. Proteome Analysis of Rheumatoid Arthritis Gut Mucosa

Author:: Bennike Tue Bjerg; Ellingsen Torkell; Glerup Henning; Bonderup Ole Kristian; Carlsen Thomas Gelsing; Meyer Michael Kruse; Bøgsted Martin; Christiansen Gunna; Birkelund Svend; Andersen Vibeke; Stensballe Allan
Source:: Journal of Proteome Research 2017 v.16 no.1 pp. 346-354
ISSN:: 1535-3907
Subject:: administered dose; antibodies; biopsy; cartilage; colon; colonoscopy; confocal microscopy; cytosol; digestive tract mucosa; dihydrofolate reductase; immunohistochemistry; immunosuppression; membrane proteins; methotrexate; peptides; proteome; proteomics; rheumatoid arthritis
Abstract:: ... Rheumatoid arthritis (RA) is an inflammatory joint disease leading to cartilage damage and ultimately impaired joint function. To gain new insight into the systemic immune manifestations of RA, we characterized the colon mucosa proteome from 11 RA-patients and 10 healthy controls. The biopsies were extracted by colonoscopy and analyzed by label-free quantitative proteomics, enabling the quantitati ...
DOI:: 10.1021/acs.jproteome.6b00598
: https://doi.org/10.1021/acs.jproteome.6b00598

76. Proteomic Analysis of Amyloid Corneal Aggregates from TGFBI-H626R Lattice Corneal Dystrophy Patient Implicates Serine-Protease HTRA1 in Mutation-Specific Pathogenesis of TGFBIp

Author:: Venkatraman Anandalakshmi; Dutta Bamaprasad; Murugan Elavazhagan; Piliang Hao; Lakshminaryanan Rajamani; Sook Yee Anita Chan; Pervushin Konstantin V.; Sze Siu Kwan; Mehta Jodhbir S.
Source:: Journal of Proteome Research 2017 v.16 no.8 pp. 2899-2913
ISSN:: 1535-3907
Subject:: amino acid substitution; amyloid; apolipoprotein E; cornea; genes; mutants; pathogenesis; patients; peptides; proteolysis; proteome; proteomics; serine proteinases; tissues
Abstract:: ... TGFBI-associated corneal dystrophies are inherited disorders caused by TGFBI gene variants that promote deposition of mutant protein (TGFBIp) as insoluble aggregates in the cornea. Depending on the type and position of amino acid substitution, the aggregates may be amyloid fibrillar, amorphous globular or both, but the molecular mechanisms that drive these different patterns of aggregation are not ...
DOI:: 10.1021/acs.jproteome.7b00188
: https://doi.org/10.1021/acs.jproteome.7b00188

77. Proteomic Analysis of Primary Human Airway Epithelial Cells Exposed to the Respiratory Toxicant Diacetyl

Author:: Foster Matthew W.; Gwinn William M.; Kelly Francine L.; Brass David M.; Valente Ashlee M.; Moseley M. Arthur; Thompson J. Will; Morgan Daniel L.; Palmer Scott M.
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 538-549
ISSN:: 1535-3907
Subject:: bronchiolitis; cilia; crosslinking; diacetyl; epithelial cells; epithelium; fibrosis; fluorescent antibody technique; humans; keratin; models; monitoring; pathogenesis; phosphopeptides; phosphorylation; proteome; proteomics; rodents; staining; toxicity; vapors
Abstract:: ... Occupational exposures to the diketone flavoring agent, diacetyl, have been associated with bronchiolitis obliterans, a rare condition of airway fibrosis. Model studies in rodents have suggested that the airway epithelium is a major site of diacetyl toxicity, but the effects of diacetyl exposure upon the human airway epithelium are poorly characterized. Here we performed quantitative LC–MS/MS-base ...
DOI:: 10.1021/acs.jproteome.6b00672
: https://doi.org/10.1021/acs.jproteome.6b00672

78. Proteomic and Bioinformatic Characterization of Extracellular Vesicles Released from Human Macrophages upon Influenza A Virus Infection

Author:: Cypryk Wojciech; Lorey Martina; Puustinen Anne; Nyman Tuula A.; Matikainen Sampsa
Source:: Journal of Proteome Research 2017 v.16 no.1 pp. 217-227
ISSN:: 1535-3907
Subject:: Influenza A virus; autophagy; bioinformatics; copper; copper metabolism; cytokines; disease outbreaks; fatty acid-binding proteins; humans; macrophages; pathogens; protein secretion; proteome; proteomics; respiratory tract diseases; ribosomes; spliceosomes
Abstract:: ... Influenza A viruses (IAVs) are aggressive pathogens that cause acute respiratory diseases and annual epidemics in humans. Host defense against IAV infection is initiated by macrophages, which are the principal effector cells of the innate immune system. We have previously shown that IAV infection of human macrophages is associated with robust secretion of proteins via conventional and unconvention ...
DOI:: 10.1021/acs.jproteome.6b00596
: https://doi.org/10.1021/acs.jproteome.6b00596

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

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

80. Quantitative Proteomics Analysis Confirmed Oxidative Metabolism Predominates in Streptomyces coelicolor versus Glycolytic Metabolism in Streptomyces lividans

Author:: Millan-Oropeza Aaron; Henry Céline; Blein-Nicolas Mélisande; Aubert-Frambourg Anne; Moussa Fathi; Bleton Jean; Virolle Marie-Jöelle
Source:: Journal of Proteome Research 2017 v.16 no.7 pp. 2597-2613
ISSN:: 1535-3907
Subject:: Streptomyces coelicolor; Streptomyces lividans; aerobiosis; amino acids; biochemical pathways; dormancy; glucose; glycolysis; oxidative stress; oxygen; proteins; proteome; proteomics; regulon; siderophores; tellurium; terpenoids
Abstract:: ... Recent physiological studies indicated that S. lividans metabolism was mainly glycolytic, whereas S. coelicolor metabolism was mainly oxidative. To determine whether such metabolic characteristics were correlated with consistent proteomics features, a comparative label-free, shotgun proteomics analysis of these strains was carried out. Among 2024 proteins identified, 360 showed significant differe ...
DOI:: 10.1021/acs.jproteome.7b00163
: https://doi.org/10.1021/acs.jproteome.7b00163

81. Quantitative Proteomics Charts the Landscape of Salmonella Carbon Metabolism within Host Epithelial Cells

Author:: Liu Yanhua; Yu Kaiwen; Zhou Fan; Ding Tao; Yang Yufei; Hu Mo; Liu Xiaoyun
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 788-797
ISSN:: 1535-3907
Subject:: Salmonella Typhimurium; biosynthesis; carbon metabolism; chemotaxis; epithelial cells; fermentation; flagellum; glycolysis; pentose phosphate cycle; proteome; proteomics; surveys; tricarboxylic acid cycle
Abstract:: ... We performed a proteomic survey of Salmonella enterica serovar Typhimurium during infection of host epithelial cells. Our data reveal substantial metabolic reshuffling of Salmonella in the host in addition to severe degeneration of bacterial flagella and chemotaxis systems. The large-scale quantitative data allowed us to chart an overview of intracellular Salmonella carbon metabolism. Notably, we ...
DOI:: 10.1021/acs.jproteome.6b00793
: https://doi.org/10.1021/acs.jproteome.6b00793

82. Quantitative Proteomics for the Comprehensive Analysis of Stress Responses of Lactobacillus paracasei subsp. paracasei F19

Author:: Schott Ann-Sophie; Behr Jürgen; Geißler Andreas J.; Kuster Bernhard; Hahne Hannes; Vogel Rudi F.
Source:: Journal of Proteome Research 2017 v.16 no.10 pp. 3816-3829
ISSN:: 1535-3907
Subject:: drying; foods; gene expression regulation; genes; genomics; lactic acid bacteria; manufacturing; microbial physiology; models; pH; prediction; proteins; proteome; proteomics; starter cultures; stress response
Abstract:: ... Lactic acid bacteria are broadly employed as starter cultures in the manufacture of foods. Upon technological preparation, they are confronted with drying stress that amalgamates numerous stress conditions resulting in losses of fitness and survival. To better understand and differentiate physiological stress responses, discover general and specific markers for the investigated stress conditions, ...
DOI:: 10.1021/acs.jproteome.7b00474
: https://doi.org/10.1021/acs.jproteome.7b00474

83. Quantitative Secretome Analysis of Activated Jurkat Cells Using Click Chemistry-Based Enrichment of Secreted Glycoproteins

Author:: Witzke Kathrin E.; Rosowski Kristin; Müller Christian; Ahrens Maike; Eisenacher Martin; Megger Dominik A.; Knobloch Jürgen; Koch Andrea; Bracht Thilo; Sitek Barbara
Source:: Journal of Proteome Research 2017 v.16 no.1 pp. 137-146
ISSN:: 1535-3907
Subject:: T-lymphocytes; biotin; blood serum; cell culture; chemistry; culture media; data collection; glycoproteins; models; protein secretion; proteome; starvation
Abstract:: ... Quantitative secretome analyses are a high-performance tool for the discovery of physiological and pathophysiological changes in cellular processes. However, serum supplements in cell culture media limit secretome analyses, but serum depletion often leads to cell starvation and consequently biased results. To overcome these limiting factors, we investigated a model of T cell activation (Jurkat cel ...
DOI:: 10.1021/acs.jproteome.6b00575
: https://doi.org/10.1021/acs.jproteome.6b00575

84. Robust, Sensitive, and Automated Phosphopeptide Enrichment Optimized for Low Sample Amounts Applied to Primary Hippocampal Neurons

Author:: Post Harm; Penning Renske; Fitzpatrick Martin A.; Garrigues Luc B.; Wu W.; MacGillavry Harold D.; Hoogenraad Casper C.; Heck Albert J. R.; Altelaar A. F. Maarten
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 728-737
ISSN:: 1535-3907
Subject:: glutamate receptors; human cell lines; iron; mitogen-activated protein kinase; neurons; neuroplasticity; phosphopeptides; protein phosphorylation; proteome; rats; stoichiometry; titanium
Abstract:: ... Because of the low stoichiometry of protein phosphorylation, targeted enrichment prior to LC–MS/MS analysis is still essential. The trend in phosphoproteome analysis is shifting toward an increasing number of biological replicates per experiment, ideally starting from very low sample amounts, placing new demands on enrichment protocols to make them less labor-intensive, more sensitive, and less pr ...
DOI:: 10.1021/acs.jproteome.6b00753
: https://doi.org/10.1021/acs.jproteome.6b00753

85. Scale-Invariant Biomarker Discovery in Urine and Plasma Metabolite Fingerprints

Author:: Zacharias Helena U.; Rehberg Thorsten; Mehrl Sebastian; Richtmann Daniel; Wettig Tilo; Oefner Peter J.; Spang Rainer; Gronwald Wolfram; Altenbuchinger Michael
Source:: Journal of Proteome Research 2017 v.16 no.10 pp. 3596-3605
ISSN:: 1535-3907
Subject:: algorithms; biomarkers; computer software; creatinine; metabolites; metabolomics; proteome; regression analysis; screening; urine
Abstract:: ... Metabolomics data is typically scaled to a common reference like a constant volume of body fluid, a constant creatinine level, or a constant area under the spectrum. Such scaling of the data, however, may affect the selection of biomarkers and the biological interpretation of results in unforeseen ways. Here, we studied how both the outcome of hypothesis tests for differential metabolite concentra ...
DOI:: 10.1021/acs.jproteome.7b00325
: https://doi.org/10.1021/acs.jproteome.7b00325

86. Sensitive and Accurate Quantitation of Phosphopeptides Using TMT Isobaric Labeling Technique

Author:: Jiang Xiaoyue; Bomgarden Ryan; Brown Joseph; Drew Devin L.; Robitaille Aaron M.; Viner Rosa; Huhmer Andreas R.
Source:: Journal of Proteome Research 2017 v.16 no.11 pp. 4244-4252
ISSN:: 1535-3907
Subject:: cell lines; epidermal growth factor receptors; insulin; insulin-like growth factor I; mass spectrometry; phosphopeptides; phosphorylation; post-translational modification; proteome; proteomics; rapamycin; signal transduction
Abstract:: ... Phosphorylation is an essential post-translational modification for regulating protein function and cellular signal transduction. Mass spectrometry (MS) combined with isobaric tandem mass tags (TMTs) has become a powerful platform for simultaneous, large-scale phospho-proteome site identification and quantitation. To improve the accuracy of isobaric tag-based quantitation in complex proteomic samp ...
DOI:: 10.1021/acs.jproteome.7b00610
: https://doi.org/10.1021/acs.jproteome.7b00610

87. Sensitive and Precise Characterization of Combinatorial Histone Modifications by Selective Derivatization Coupled with RPLC-EThcD-MS/MS

Author:: Liao Rijing; Zheng Dan; Nie Aiying; Zhou Shaolian; Deng Haibing; Gao Yuan; Yang Pengyuan; Yu Yanyan; Tan Lin; Qi Wei; Wu Jiaxi; Li En; Yi Wei
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 780-787
ISSN:: 1535-3907
Subject:: cation exchange; derivatization; dissociation; drug therapy; electron transfer; energy; epigenetics; histones; hydrophilic interaction chromatography; hydrophobicity; ionization; mass spectrometry; neoplasm cells; peptides; post-translational modification; propionic acid; proteome; reversed-phase liquid chromatography
Abstract:: ... Deciphering the combinatorial histone codes has been a long-standing interest in the epigenetics field, which requires the reliable and robust characterization of the post-translational modifications (PTMs) coexisting on histones. To this end, weak cation exchange hydrophilic interaction liquid chromatography is commonly used in middle-down liquid chromatography–mass spectrometry approaches for on ...
DOI:: 10.1021/acs.jproteome.6b00788
: https://doi.org/10.1021/acs.jproteome.6b00788

88. Serum Protein Markers for the Early Detection of Lung Cancer: A Focus on Autoantibodies

Author:: Broodman Ingrid; Lindemans Jan; van Sten Jenny; Bischoff Rainer; Luider Theo
Source:: Journal of Proteome Research 2017 v.16 no.1 pp. 3-13
ISSN:: 1535-3907
Subject:: antigens; autoantibodies; biomarkers; blood proteins; body fluids; computed tomography; image analysis; immune system; lung neoplasms; lungs; monitoring; mortality; patients; proteome; screening
Abstract:: ... Lung cancer has the highest mortality rate among cancer patients in the world, in particular because most patients are only diagnosed at an advanced and noncurable stage. Computed tomography (CT) screening on high-risk individuals has shown that early detection could reduce the mortality rate. However, the still high false-positive rate of CT screening may harm healthy individuals because of unnec ...
DOI:: 10.1021/acs.jproteome.6b00559
: https://doi.org/10.1021/acs.jproteome.6b00559

89. Serum Proteomic Variability Associated with Clinical Phenotype in Familial Transthyretin Amyloidosis (ATTRm)

Author:: Chan Gloria G.; Koch Clarissa M.; Connors Lawreen H.
Source:: Journal of Proteome Research 2017 v.16 no.11 pp. 4104-4112
ISSN:: 1535-3907
Subject:: amyloid; amyloidosis; biomarkers; blood serum; cardiomyopathy; disulfide bonds; genes; glycoproteins; glycosylation; heart; males; mass spectrometry; monitoring; patients; phenotype; point mutation; prealbumin; proteome; proteomics; signal peptide
Abstract:: ... Transthyretin (TTR), normally a plasma circulating protein, can become misfolded and aggregated, ultimately leading to extracellular deposition of amyloid fibrils usually targeted to heart or nerve tissues. Referred to as TTR-associated amyloidoses (ATTR), this group of diseases is frequently life threatening and fatal if untreated. ATTR, caused by amyloid-forming variant TTR proteins (ATTRm) that ...
DOI:: 10.1021/acs.jproteome.7b00479
: https://doi.org/10.1021/acs.jproteome.7b00479

90. Sexual Dimorphism, Age, and Fat Mass Are Key Phenotypic Drivers of Proteomic Signatures

Author:: Curran Aoife M.; Fogarty Draper Colleen; Scott-Boyer Marie-Pier; Valsesia Armand; Roche Helen M.; Ryan Miriam F.; Gibney Michael J.; Kutmon Martina; Evelo Chris T.; Coort Susan L.; Astrup Arne; Saris Wim H.; Brennan Lorraine; Kaput Jim
Source:: Journal of Proteome Research 2017 v.16 no.11 pp. 4122-4133
ISSN:: 1535-3907
Subject:: biomarkers; blood proteins; coagulation; complement; decision making; diagnostic techniques; females; males; oligonucleotides; phenotype; prediction; proteome; proteomics; sexual dimorphism
Abstract:: ... Validated protein biomarkers are needed for assessing health trajectories, predicting and subclassifying disease, and optimizing diagnostic and therapeutic clinical decision-making. The sensitivity, specificity, accuracy, and precision of single or combinations of protein biomarkers may be altered by differences in physiological states limiting the ability to translate research results to clinical ...
DOI:: 10.1021/acs.jproteome.7b00501
: https://doi.org/10.1021/acs.jproteome.7b00501

91. Symbiotic Interplay of Fungi, Algae, and Bacteria within the Lung Lichen Lobaria pulmonaria L. Hoffm. as Assessed by State-of-the-Art Metaproteomics

Author:: Eymann Christine; Lassek Christian; Wegner Uwe; Bernhardt Jörg; Fritsch Ole Arno; Fuchs Stephan; Otto Andreas; Albrecht Dirk; Schiefelbein Ulf; Cernava Tomislav; Aschenbrenner Ines; Berg Gabriele; Grube Martin; Riedel Katharina
Source:: Journal of Proteome Research 2017 v.16 no.6 pp. 2160-2173
ISSN:: 1535-3907
Subject:: Chlorophyta; Cyanobacteria; Lobaria; Rhizobiales; algae; algal proteins; bacteria; fungal proteins; fungi; hosts; lichens; longevity; lungs; models; nitrogen fixation; nitrogenase; photosynthesis; physiological transport; proteome; symbionts; symbiosis
Abstract:: ... Lichens are recognized by macroscopic structures formed by a heterotrophic fungus, the mycobiont, which hosts internal autotrophic photosynthetic algal and/or cyanobacterial partners, referred to as the photobiont. We analyzed the structure and functionality of the entire lung lichen Lobaria pulmonaria L. Hoffm. collected from two different sites by state-of-the-art metaproteomics. In addition to ...
DOI:: 10.1021/acs.jproteome.6b00974
: https://doi.org/10.1021/acs.jproteome.6b00974

92. Synaptosomal Proteome of the Orbitofrontal Cortex from Schizophrenia Patients Using Quantitative Label-Free and iTRAQ-Based Shotgun Proteomics

Author:: Velásquez Erika; Nogueira Fabio C. S.; Velásquez Ingrid; Schmitt Andrea; Falkai Peter; Domont Gilberto B.; Martins-de-Souza Daniel
Source:: Journal of Proteome Research 2017 v.16 no.12 pp. 4481-4494
ISSN:: 1535-3907
Subject:: apoptosis; calcium signaling; cytochrome c; endoplasmic reticulum stress; human behavior; humans; membrane proteins; patients; prefrontal cortex; protein kinases; proteome; proteomics; quantitative analysis; schizophrenia; social behavior; statistical analysis; synaptosomes
Abstract:: ... Schizophrenia is a chronic and incurable neuropsychiatric disorder that affects about one percent of the world population. The proteomic characterization of the synaptosome fraction of the orbitofrontal cortex is useful for providing valuable information about the molecular mechanisms of synaptic functions in these patients. Quantitative analyses of synaptic proteins were made with eight paranoid ...
DOI:: 10.1021/acs.jproteome.7b00422
: https://doi.org/10.1021/acs.jproteome.7b00422

93. System-Wide Quantitative Proteomics of the Metabolic Syndrome in Mice: Genotypic and Dietary Effects

Author:: Terfve Camille; Sabidó Eduard; Wu Yibo; Gonçalves Emanuel; Choi Meena; Vaga Stefania; Vitek Olga; Saez-Rodriguez Julio; Aebersold Ruedi
Source:: Journal of Proteome Research 2017 v.16 no.2 pp. 831-841
ISSN:: 1535-3907
Subject:: data collection; experimental design; mass spectrometry; metabolic syndrome; metabolism; mice; proteins; proteome; proteomics; quantitative analysis; triacylglycerols
Abstract:: ... Advances in mass spectrometry have made the quantitative measurement of proteins across multiple samples a reality, allowing for the study of complex biological systems such as the metabolic syndrome. Although the deregulation of lipid metabolism and increased hepatic storage of triacylglycerides are known to play a part in the onset of the metabolic syndrome, its molecular basis and dependency on ...
DOI:: 10.1021/acs.jproteome.6b00815
: https://doi.org/10.1021/acs.jproteome.6b00815

94. Systematic Analysis of Lysine Acetylation in the Halophilic Archaeon Haloferax mediterranei

Author:: Liu Jingfang; Wang Qian; Jiang Xiongjian; Yang Haibo; Zhao Dahe; Han Jing; Luo Yuanming; Xiang Hua
Source:: Journal of Proteome Research 2017 v.16 no.9 pp. 3229-3241
ISSN:: 1535-3907
Subject:: Haloferax mediterranei; acetylation; bacteria; bioinformatics; biosynthesis; carbon metabolism; carbon sequestration; cytoplasm; energy; enzymes; eukaryotic cells; lysine; models; mutation; post-translational modification; proteins; proteome; surveys
Abstract:: ... Lysine acetylation is a reversible and highly regulated post-translational modification that plays a critical role in regulating many aspects of cellular processes, both in bacteria and in eukaryotes. However, this modification has not been systematically studied in archaea. Herein, we report the lysine acetylome of a model haloarchaeon, Haloferax mediterranei. Using immunoaffinity enrichment and ...
DOI:: 10.1021/acs.jproteome.7b00222
: https://doi.org/10.1021/acs.jproteome.7b00222

95. Systematic Comparison of False-Discovery-Rate-Controlling Strategies for Proteogenomic Search Using Spike-in Experiments

Author:: Li Honglan; Park Jonghun; Kim Hyunwoo; Hwang Kyu-Baek; Paek Eunok
Source:: Journal of Proteome Research 2017 v.16 no.6 pp. 2231-2239
ISSN:: 1535-3907
Subject:: data collection; human cell lines; peptides; proteome; proteomics
Abstract:: ... Proteogenomic searches are useful for novel peptide identification from tandem mass spectra. Usually, separate and multistage approaches are adopted to accurately control the false discovery rate (FDR) for proteogenomic search. Their performance on novel peptide identification has not been thoroughly evaluated, however, mainly due to the difficulty in confirming the existence of identified novel p ...
DOI:: 10.1021/acs.jproteome.7b00033
: https://doi.org/10.1021/acs.jproteome.7b00033

96. Systems Metabolomics for Prediction of Metabolic Syndrome

Author:: Pujos-Guillot Estelle; Brandolini Marion; Pétéra Mélanie; Grissa Dhouha; Joly Charlotte; Lyan Bernard; Herquelot Éléonore; Czernichow Sébastien; Zins Marie; Goldberg Marcel; Comte Blandine
Source:: Journal of Proteome Research 2017 v.16 no.6 pp. 2262-2272
ISSN:: 1535-3907
Subject:: biomarkers; eating habits; males; metabolic syndrome; metabolites; metabolomics; models; phenotype; prediction; proteome
Abstract:: ... The evolution of human health is a continuum of transitions, involving multifaceted processes at multiple levels, and there is an urgent need for integrative biomarkers that can characterize and predict progression toward disease development. The objective of this work was to perform a systems metabolomics approach to predict metabolic syndrome (MetS) development. A case-control design was used wi ...
DOI:: 10.1021/acs.jproteome.7b00116
: https://doi.org/10.1021/acs.jproteome.7b00116

97. Targeted Proteomics Predicts a Sustained Complete-Response after Transarterial Chemoembolization and Clinical Outcomes in Patients with Hepatocellular Carcinoma: A Prospective Cohort Study

Author:: Yu Su Jong; Kim Hyunsoo; Min Hophil; Sohn Areum; Cho Young Youn; Yoo Jeong-Ju; Lee Dong Hyeon; Cho Eun Ju; Lee Jeong-Hoon; Gim Jungsoo; Park Taesung; Kim Yoon Jun; Kim Chung Yong; Yoon Jung-Hwan; Kim Youngsoo
Source:: Journal of Proteome Research 2017 v.16 no.3 pp. 1239-1248
ISSN:: 1535-3907
Subject:: adjuvants; biomarkers; blood serum; cohort studies; confidence interval; hepatoma; models; multivariate analysis; patients; prediction; proteins; proteome; proteomics; survival rate; therapeutics
Abstract:: ... This study was aimed to identify blood-based biomarkers to predict a sustained complete response (CR) after transarterial chemoembolization (TACE) using targeted proteomics. Consecutive patients with HCC who had undergone TACE were prospectively enrolled (training (n = 100) and validation set (n = 80)). Serum samples were obtained before and 6 months after TACE. Treatment responses were evaluated ...
DOI:: 10.1021/acs.jproteome.6b00833
: https://doi.org/10.1021/acs.jproteome.6b00833

98. The Hybrid Search: A Mass Spectral Library Search Method for Discovery of Modifications in Proteomics

Author:: Burke Meghan C.; Mirokhin Yuri A.; Tchekhovskoi Dmitrii V.; Markey Sanford P.; Heidbrink Thompson Jenny; Larkin Christopher; Stein Stephen E.
Source:: Journal of Proteome Research 2017 v.16 no.5 pp. 1924-1935
ISSN:: 1535-3907
Subject:: Chinese hamsters; amino acid sequences; amino acids; animal ovaries; databases; ions; methodology; peptides; proteome; proteomics
Abstract:: ... We present a mass spectral library-based method to identify tandem mass spectra of peptides that contain unanticipated modifications and amino acid variants. We describe this as a “hybrid” method because it combines matching both ion m/z and mass losses. The mass loss is the difference between the mass of an ion peak and the mass of its precursor. This difference, termed DeltaMass, is used to shif ...
DOI:: 10.1021/acs.jproteome.6b00988
: https://doi.org/10.1021/acs.jproteome.6b00988

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

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

100. Ultradeep Lysine Crotonylome Reveals the Crotonylation Enhancement on Both Histones and Nonhistone Proteins by SAHA Treatment

Author:: Wu Quan; Li Wenting; Wang Chi; Fan Pingsheng; Cao Lejie; Wu Zhiwei; Wang Fengsong
Source:: Journal of Proteome Research 2017 v.16 no.10 pp. 3664-3671
ISSN:: 1535-3907
Subject:: acetylation; bioinformatics; data collection; enzyme activity; histone deacetylase; histones; lysine; post-translational modification; proteome; transferases
Abstract:: ... Lysine crotonylation is a newly discovered protein post-translational modification and was reported to share transferases and deacylases with lysine acetylation. The acetyltransferase p300 was reported to also contain crotonyltransferase activity, and class I histone deacetylases were demonstrated to be the major histone decrotonylases. However, the decrotonylases for nonhistone proteins are uncle ...
DOI:: 10.1021/acs.jproteome.7b00380
: https://doi.org/10.1021/acs.jproteome.7b00380

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1. A Computational Selection of Metabolite Biomarkers Using Emerging Pattern Mining: A Case Study in Human Hepatocellular Carcinoma

2. A Shotgun Proteomics Approach Reveals a New Toxic Role for Alzheimer’s Disease Aβ Peptide: Spliceosome Impairment

3. Absolute Quantification of Human Milk Caseins and the Whey/Casein Ratio during the First Year of Lactation

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

5. Acute Consumption of Flavan-3-ol-Enriched Dark Chocolate Affects Human Endogenous Metabolism

6. Alterations in the Salivary Proteome and N-Glycome of Sjögren’s Syndrome Patients

7. Aminoquinoline Fluorescent Labels Obstruct Efficient Removal of N-Glycan Core α(1–6) Fucose by Bovine Kidney α-l-Fucosidase (BKF)

8. Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins

9. Application of Metabolic Profiling to Abdominal Aortic Aneurysm Research

10. Application of Nanosecond Laser Photolysis Protein Footprinting to Study EGFR Activation by EGF in Cells

11. Arginine (Di)methylated Human Leukocyte Antigen Class I Peptides Are Favorably Presented by HLA-B*07

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

13. Brain Membrane Proteome and Phosphoproteome Reveal Molecular Basis Associating with Nursing and Foraging Behaviors of Honeybee Workers

14. Candida albicans Modifies the Protein Composition and Size Distribution of THP-1 Macrophage-Derived Extracellular Vesicles

15. Characterization of the Extracellular Matrix of Normal and Diseased Tissues Using Proteomics

16. Combined Clinical Phenotype and Lipidomic Analysis Reveals the Impact of Chronic Kidney Disease on Lipid Metabolism

17. Comfortably Numb and Back: Plasma Metabolomics Reveals Biochemical Adaptations in the Hibernating 13-Lined Ground Squirrel

18. Comparison of False Discovery Rate Control Strategies for Variant Peptide Identifications in Shotgun Proteogenomics

19. Comprehensive Lipoprotein Characterization Using Lipidomics Analysis of Human Plasma

20. Comprehensive Metabolomic and Lipidomic Profiling of Human Kidney Tissue: A Platform Comparison

21. Comprehensive Metabolomics Study To Assess Longitudinal Biochemical Changes and Potential Early Biomarkers in Nonobese Diabetic Mice That Progress to Diabetes

22. Comprehensive Proteomics Analysis Reveals Metabolic Reprogramming of Tumor-Associated Macrophages Stimulated by the Tumor Microenvironment

23. Cyclophilin B Deficiency Causes Abnormal Dentin Collagen Matrix

24. Decoding the Effect of Isobaric Substitutions on Identifying Missing Proteins and Variant Peptides in Human Proteome

25. Differences between Platelets Derived from Neonatal Cord Blood and Adult Peripheral Blood Assessed by Mass Spectrometry

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

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

28. Evaluating the Characteristics of Reporter Ion Signal Acquired in the Orbitrap Analyzer for Isobaric Mass Tag Proteome Quantification Experiments

29. Evaluation of FASP, SP3, and iST Protocols for Proteomic Sample Preparation in the Low Microgram Range

30. Exhaustively Identifying Cross-Linked Peptides with a Linear Computational Complexity

31. Experimental Design in Clinical ‘Omics Biomarker Discovery

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

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

34. Global Profiling of Metabolite and Lipid Soluble Microbial Products in Anaerobic Wastewater Reactor Supernatant Using UPLC–MSE

35. Glycosylation Changes Triggered by the Differentiation of Monocytic THP-1 Cell Line into Macrophages

36. Glycosylation Changes in Serum Proteins Identify Patients with Pancreatic Cancer

37. Hydrophobic Interaction Chromatography for Bottom-Up Proteomics Analysis of Single Proteins and Protein Complexes

38. IL- 6 Linkage to Exercise-Induced Shifts in Lipid-Related Metabolites: A Metabolomics-Based Analysis

39. Identification and Validation of Human Missing Proteins and Peptides in Public Proteome Databases: Data Mining Strategy

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

41. Identification of Genes Associated with Breast Cancer Metastasis to Bone on a Protein–Protein Interaction Network with a Shortest Path Algorithm

42. Identification of Novel Protein Expression Changes Following Cisplatin Treatment and Application to Combination Therapy

43. Identification of Urinary Food Intake Biomarkers for Milk, Cheese, and Soy-Based Drink by Untargeted GC-MS and NMR in Healthy Humans

44. Identifications of Putative PKA Substrates with Quantitative Phosphoproteomics and Primary-Sequence-Based Scoring

45. Immuno-affinity Capture Followed by TMPP N-Terminus Tagging to Study Catabolism of Therapeutic Proteins

46. Impact of the Niemann–Pick c1 Gene Mutation on the Total Cellular Glycomics of CHO Cells

47. Impact of the Pd2Spermine Chelate on Osteosarcoma Metabolism: An NMR Metabolomics Study

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

49. Improvements in Mass Spectrometry Assay Library Generation for Targeted Proteomics

50. In Situ Characterization of Tissue-Resident Immune Cells by MALDI Mass Spectrometry Imaging

51. Infections with the Sexually Transmitted Pathogen Nosema apis Trigger an Immune Response in the Seminal Fluid of Honey Bees (Apis mellifera)

52. Influence of Ingesting a Flavonoid-Rich Supplement on the Metabolome and Concentration of Urine Phenolics in Overweight/Obese Women

53. Integrative Analysis of Renal Ischemia/Reperfusion Injury and Remote Ischemic Preconditioning in Mice

54. Intra- and Interskeletal Proteome Variations in Fresh and Buried Bones

55. Intrinsically Disordered Proteins as Important Players during Desiccation Stress of Soybean Radicles

56. Large-Scale Identification of Protein Crotonylation Reveals Its Role in Multiple Cellular Functions

57. Large-Scale SRM Screen of Urothelial Bladder Cancer Candidate Biomarkers in Urine

58. Limiting the Hydrolysis and Oxidation of Maleimide–Peptide Adducts Improves Detection of Protein Thiol Oxidation

59. Lycopene Prevents Mitochondrial Dysfunction during d-Galactosamine/Lipopolysaccharide-Induced Fulminant Hepatic Failure in Albino Rats

60. MALDI versus ESI: The Impact of the Ion Source on Peptide Identification

61. Malonylome Analysis Reveals the Involvement of Lysine Malonylation in Metabolism and Photosynthesis in Cyanobacteria

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

63. Metabolic Pathways Regulated by Chitosan Contributing to Drought Resistance in White Clover

64. Metabolic Phenotype of Obesity in a Saudi Population

65. Metabolic Response to Everolimus in Patient-Derived Triple-Negative Breast Cancer Xenografts

66. Metabolomic Fingerprinting in Various Body Fluids of a Diet-Controlled Clinical Smoking Cessation Study Using a Validated GC-TOF-MS Metabolomics Platform

67. Metabolomics-Based Elucidation of Active Metabolic Pathways in Erythrocytes and HSC-Derived Reticulocytes

68. Minimizing Laboratory-Induced Decay in Bone Proteomics

69. Model for Quality Control of Allergen Products with Mass Spectrometry

70. Molecular Dynamics Information Improves cis-Peptide-Based Function Annotation of Proteins