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1. 1H NMR Metabolic Profiling of Earthworm (Eisenia fetida) Coelomic Fluid, Coelomocytes, and Tissue: Identification of a New MetaboliteMalylglutamate

Author:
Griffith Corey M.; Williams Preston B.; Tinoco Luzineide W.; Dinges Meredith M.; Wang Yinsheng; Larive Cynthia K.
Source:
Journal of Proteome Research 2017 v.16 no.9 pp. 3407-3418
ISSN:
1535-3907
Subject:
Eisenia fetida; chelating agents; earthworms; ecotoxicology; electrolytes; malates; metabolism; metabolites; metabolomics; nuclear magnetic resonance spectroscopy; proteome; trigonelline
Abstract:
... Earthworm metabolism is recognized as a useful tool for monitoring environmental insults and measuring ecotoxicity, yet extensive earthworm metabolic profiling using ¹H nuclear magnetic resonance (NMR) spectroscopy has been limited in scope. This study aims to expand the embedded metabolic material in earthworm coelomic fluid, coelomocytes, and tissue to aid systems toxicology research. Fifty-nine ...
DOI:
10.1021/acs.jproteome.7b00439
PubMed:
28753027
PubMed Central:
PMC5585853

2. 1H NMR To Evaluate the Metabolome of Bronchoalveolar Lavage Fluid (BALf) in Bronchiolitis Obliterans Syndrome (BOS): Toward the Development of a New Approach for Biomarker Identification

Author:
Ciaramelli Carlotta; Fumagalli Marco; Viglio Simona; Bardoni Anna Maria; Piloni Davide; Meloni Federica; Iadarola Paolo; Airoldi Cristina
Source:
Journal of Proteome Research 2017 v.16 no.4 pp. 1669-1682
ISSN:
1535-3907
Subject:
amino acids; biomarkers; bronchiolitis; disaccharides; inflammation; lungs; metabolites; metabolome; models; monitoring; nuclear magnetic resonance spectroscopy; nucleotides; patients; phospholipids; prediction; proteome; screening; statistical analysis; tricarboxylic acid cycle
Abstract:
... This report describes the application of NMR spectroscopy to the profiling of metabolites in bronchoalveolar lavage fluid (BALf) of lung transplant recipients without bronchiolitis obliterans syndrome (BOS) (stable, S, n = 10), and with BOS at different degrees of severity (BOS 0p, n = 10; BOS I, n = 10). Through the fine-tuning of a number of parameters concerning both sample preparation/processi ...
DOI:
10.1021/acs.jproteome.6b01038

3. 1H NMR-Based Global Metabolic Studies of Pseudomonas aeruginosa upon Exposure of the Quorum Sensing Inhibitor Resveratrol

Author:
Chen Tongtong; Sheng Jiyang; Fu Yonghong; Li Minghui; Wang Junsong; Jia Ai-Qun
Source:
Journal of Proteome Research 2017 v.16 no.2 pp. 824-830
ISSN:
1535-3907
Subject:
Pseudomonas aeruginosa; amino acids; anaerobiosis; antioxidant activity; cytotoxicity; drugs; energy; gene expression; gene expression regulation; metabolic studies; metabolites; nuclear magnetic resonance spectroscopy; oxidative stress; protein synthesis; proteome; pyocyanin; quorum sensing; resveratrol; tricarboxylic acid cycle; virulence
Abstract:
... Quorum sensing (QS) is a process of bacterial communication that has been a novel target for drug discovery. Pyocyanin quantification assay confirmed that resveratrol was an effective quorum sensing inhibitor (QSI) against Pseudomonas aeruginosa PAO1. In this study, the global metabolite changes of P. aeruginosa PAO1 exposed to QSI resveratrol were investigated by ¹H NMR spectroscopy. A total of 4 ...
DOI:
10.1021/acs.jproteome.6b00800

4. 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

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

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

6. 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

7. Accurate Identification of Unknown and Known Metabolic Mixture Components by Combining 3D NMR with Fourier Transform Ion Cyclotron Resonance Tandem Mass Spectrometry

Author:
Wang Cheng; He Lidong; Li Da-Wei; Bruschweiler-Li Lei; Marshall Alan G.; Brüschweiler Rafael
Source:
Journal of Proteome Research 2017 v.16 no.10 pp. 3774-3786
ISSN:
1535-3907
Subject:
Escherichia coli; chemical structure; databases; metabolites; metabolomics; models; nuclear magnetic resonance spectroscopy; proteome; tandem mass spectrometry
Abstract:
... Metabolite identification in metabolomics samples is a key step that critically impacts downstream analysis. We recently introduced the SUMMIT NMR/mass spectrometry (MS) hybrid approach for the identification of the molecular structure of unknown metabolites based on the combination of NMR, MS, and combinatorial cheminformatics. Here, we demonstrate the feasibility of the approach for an untargete ...
DOI:
10.1021/acs.jproteome.7b00457
PubMed:
28795575
PubMed Central:
PMC5663437

8. 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

9. Activated Ion-Electron Transfer Dissociation Enables Comprehensive Top-Down Protein Fragmentation

Author:
Riley Nicholas M.; Westphall Michael S.; Coon Joshua J.
Source:
Journal of Proteome Research 2017 v.16 no.7 pp. 2653-2659
ISSN:
1535-3907
Subject:
amino acid sequences; dissociation; ions; proteins; proteome
Abstract:
... Here we report the first demonstration of near-complete sequence coverage of intact proteins using activated ion-electron transfer dissociation (AI-ETD), a method that leverages concurrent infrared photoactivation to enhance electron-driven dissociation. AI-ETD produces mainly c/z-type product ions and provides comprehensive (77–97%) protein sequence coverage, outperforming HCD, ETD, and EThcD for ...
DOI:
10.1021/acs.jproteome.7b00249
PubMed:
28608681
PubMed Central:
PMC5555583

10. Activation of Human Peripheral Blood Eosinophils by Cytokines in a Comparative Time-Course Proteomic/Phosphoproteomic Study

Author:
Soman Kizhake V.; Stafford Susan J.; Pazdrak Konrad; Wu Zheng; Luo Xuemei; White Wendy I.; Wiktorowicz John E.; Calhoun William J.; Kurosky Alexander
Source:
Journal of Proteome Research 2017 v.16 no.8 pp. 2663-2679
ISSN:
1535-3907
Subject:
asthma; eosinophils; flow cytometry; granulocyte-macrophage colony-stimulating factor; humans; interleukin-3; interleukin-5; mass spectrometry; multivariate analysis; phosphoproteins; phosphorylation; protein synthesis; proteome; proteomics; signal transduction; two-dimensional gel electrophoresis
Abstract:
... Activated eosinophils contribute to airway dysfunction and tissue remodeling in asthma and thus are considered to be important factors in asthma pathology. We report here comparative proteomic and phosphoproteomic changes upon activation of eosinophils using eight cytokines individually and in selected cytokine combinations in time-course reactions. Differential protein and phosphoprotein expressi ...
DOI:
10.1021/acs.jproteome.6b00367

11. 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

12. Advancing Top-down Analysis of the Human Proteome Using a Benchtop Quadrupole-Orbitrap Mass Spectrometer

Author:
Fornelli Luca; Durbin Kenneth R.; Fellers Ryan T.; Early Bryan P.; Greer Joseph B.; LeDuc Richard D.; Compton Philip D.; Kelleher Neil L.
Source:
Journal of Proteome Research 2017 v.16 no.2 pp. 609-618
ISSN:
1535-3907
Subject:
computer software; data collection; fibroblasts; humans; mass spectrometry; proteins; proteome; proteomics; spectrometers
Abstract:
... Over the past decade, developments in high resolution mass spectrometry have enabled the high throughput analysis of intact proteins from complex proteomes, leading to the identification of thousands of proteoforms. Several previous reports on top-down proteomics (TDP) relied on hybrid ion trap–Fourier transform mass spectrometers combined with data-dependent acquisition strategies. To further red ...
DOI:
10.1021/acs.jproteome.6b00698
PubMed:
28152595
PubMed Central:
PMC5395285

13. Aggregatibacter actinomycetemcomitans Growth in Biofilm versus Planktonic State: Differential Expression of Proteins

Author:
Llama-Palacios Arancha; Potupa Oksana; Sánchez María C.; Figuero Elena; Herrera David; Sanz Mariano
Source:
Journal of Proteome Research 2017 v.16 no.9 pp. 3158-3167
ISSN:
1535-3907
Subject:
Actinobacillus actinomycetemcomitans; Western blotting; adenylate kinase; bacteria; biofilm; biosynthesis; blood serum; gene expression regulation; humans; outer membrane proteins; pathogenesis; patients; periodontitis; plankton; proteome; proteomics; virulence
Abstract:
... Aggregatibacter actinomycetemcomitans (Aa) is a pathogenic bacterium residing in the subgingival plaque biofilm strongly associated with the pathogenesis of periodontitis. The aim of this investigation was to study the protein differential expression of Aa when growing on biofilm compared with planktonic state using proteomic analysis by the 2D-DIGE system. Eighty-seven proteins were differentiall ...
DOI:
10.1021/acs.jproteome.7b00127

14. 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

15. 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

16. Amniotic Fluid and Maternal Serum Metabolic Signatures in the Second Trimester Associated with Preterm Delivery

Author:
Virgiliou Christina; Gika Helen G.; Witting Michael; Bletsou Anna A.; Athanasiadis Apostolos; Zafrakas Menelaos; Thomaidis Nikolaos S.; Raikos Nikolaos; Makrydimas Georgios; Theodoridis Georgios A.
Source:
Journal of Proteome Research 2017 v.16 no.2 pp. 898-910
ISSN:
1535-3907
Subject:
amniotic fluid; biomarkers; blood serum; energy metabolism; fetal development; glutamic acid; glutamine; lipids; metabolites; metabolomics; pregnancy outcome; pregnant women; proteome; pyruvic acid
Abstract:
... Preterm delivery (PTD) represents a major health problem that occurs in 1 in 10 births. The hypothesis of the present study was that the metabolic profile of different biological fluids, obtained from pregnant women during the second trimester of gestation, could allow useful correlations with pregnancy outcome. Holistic and targeted metabolomics approaches were applied for the complementary asses ...
DOI:
10.1021/acs.jproteome.6b00845

17. Analysis of O-Glycopeptides by Acetone Enrichment and Capillary Electrophoresis-Mass Spectrometry

Author:
Mancera-Arteu Montserrat; Giménez Estela; Benavente Fernando; Barbosa José; Sanz-Nebot Victòria
Source:
Journal of Proteome Research 2017 v.16 no.11 pp. 4166-4176
ISSN:
1535-3907
Subject:
acetone; apolipoprotein C-III; biomarkers; biopharmaceuticals; capillary electrophoresis; cattle; digestion; discriminant analysis; erythropoietin; humans; least squares; mass spectrometry; ovalbumin; physicochemical properties; principal component analysis; proteome; quality control
Abstract:
... Acetone precipitation was evaluated as a rapid, simple, low-cost, and efficient method for the selective purification of O-glycopeptides from enzymatic digests of glycoproteins. Ovalbumin (OVA), human and bovine α₁-acid glycoprotein (hAGP and bAGP), human apolipoprotein C–III (APO-C3), and recombinant human erythropoietin (rhEPO) were used to obtain enzymatic digests with a broad and varied set of ...
DOI:
10.1021/acs.jproteome.7b00524

18. Analysis of Reproducibility of Proteome Coverage and Quantitation Using Isobaric Mass Tags (iTRAQ and TMT)

Author:
Casey Tammy M.; Khan Javed M.; Bringans Scott D.; Koudelka Tomas; Takle Pari S.; Downs Rachael A.; Livk Andreja; Syme Robert A.; Tan Kar-Chun; Lipscombe Richard J.
Source:
Journal of Proteome Research 2017 v.16 no.2 pp. 384-392
ISSN:
1535-3907
Subject:
computer software; protein synthesis; proteins; proteome; quantitative analysis
Abstract:
... This study aimed to compare the depth and reproducibility of total proteome and differentially expressed protein coverage in technical duplicates and triplicates using iTRAQ 4-plex, iTRAQ 8-plex, and TMT 6-plex reagents. The analysis was undertaken because comprehensive comparisons of isobaric mass tag reproducibility have not been widely reported in the literature. The highest number of proteins ...
DOI:
10.1021/acs.jproteome.5b01154

19. Analysis of Stage-Specific Protein Expression during Babesia Bovis Development within Female Rhipicephalus Microplus

Author:
Johnson Wendell C.; Taus Naomi S.; Reif Kathryn E.; Bohaliga Gamila A.R.; Kappmeyer Lowell S.; Ueti Massaro W.
Source:
Journal of Proteome Research 2017 v.16 no.3 pp. 1327-1338
ISSN:
1535-3907
Subject:
Babesia bovis; Protozoa; Rhipicephalus microplus; antibodies; asexual reproduction; blood; cattle; diploidy; disease vectors; females; fluorescent antibody technique; gel electrophoresis; genes; haploidy; hosts; mass spectrometry; pathogens; protein synthesis; proteins; proteome; proteomics; ticks; transcription (genetics); vaccines
Abstract:
... Arthropod-borne protozoan pathogens have a complex life cycle that includes asexual reproduction of haploid stages in mammalian hosts and the development of diploid stages in invertebrate hosts. The ability of pathogens to invade, survive, and replicate within distinct cell types is required to maintain their life cycle. In this study, we describe a comparative proteomic analysis of a cattle patho ...
DOI:
10.1021/acs.jproteome.6b00947
CHORUS:
10.1021/acs.jproteome.6b00947

20. Annotation of the Domestic Pig Genome by Quantitative Proteogenomics

Author:
Marx Harald; Hahne Hannes; Ulbrich Susanne E.; Schnieke Angelika; Rottmann Oswald; Frishman Dmitrij; Kuster Bernhard
Source:
Journal of Proteome Research 2017 v.16 no.8 pp. 2887-2898
ISSN:
1535-3907
Subject:
Sus scrofa; animal models; applied research; genes; humans; juveniles; mass spectrometry; pregnancy; protein synthesis; proteins; proteome; proteomics; swine; xenotransplantation
Abstract:
... The pig is one of the earliest domesticated animals in the history of human civilization and represents one of the most important livestock animals. The recent sequencing of the Sus scrofa genome was a major step toward the comprehensive understanding of porcine biology, evolution, and its utility as a promising large animal model for biomedical and xenotransplantation research. However, the funct ...
DOI:
10.1021/acs.jproteome.7b00184