Journal of Proteome Research (J PROTEOME RES)

Publisher: American Chemical Society

Journal description

The Journal of Proteome Research (JPR) provides content encompassing all aspects of systems-oriented, global protein analysis and function, emphasizing the synergy between physical and life sciences resulting in a multi-disciplinary approach to the understanding of biological processes. JPR integrates the fields of chemistry, mathematics, applied physics, biology, and medicine in order to better understand the function of proteins in biological systems. In addition to publishing original peer-reviewed research papers, JPR also publishes research highlights, current events, book and software reviews, and a calendar of upcoming short courses and symposia of interest to proteomic scientists.

Current impact factor: 4.25

Impact Factor Rankings

2016 Impact Factor Available summer 2017
2014 / 2015 Impact Factor 4.245
2013 Impact Factor 5.001
2012 Impact Factor 5.056
2011 Impact Factor 5.113
2010 Impact Factor 5.46
2009 Impact Factor 5.132
2008 Impact Factor 5.684
2007 Impact Factor 5.675
2006 Impact Factor 5.151
2005 Impact Factor 6.901
2004 Impact Factor 6.917
2003 Impact Factor 5.611
2002 Impact Factor

Impact factor over time

Impact factor

Additional details

5-year impact 4.48
Cited half-life 4.70
Immediacy index 0.90
Eigenfactor 0.06
Article influence 1.29
Website Journal of Proteome Research website
Other titles Journal of proteome research (Online), Journal of proteome research, Proteome research, JPR
ISSN 1535-3893
OCLC 47082841
Material type Document, Periodical, Internet resource
Document type Internet Resource, Computer File, Journal / Magazine / Newspaper

Publisher details

American Chemical Society

  • Pre-print
    • Author cannot archive a pre-print version
  • Restrictions
    • Must obtain written permission from Editor
    • Must not violate ACS ethical Guidelines
  • Post-print
    • Author cannot archive a post-print version
  • Restrictions
    • If mandated by funding agency or employer/ institution
    • If mandated to deposit before 12 months, must obtain waiver from Institution/Funding agency or use AuthorChoice
    • 12 months embargo
  • Conditions
    • On author's personal website, pre-print servers, institutional website, institutional repositories or subject repositories
    • Non-Commercial
    • Must be accompanied by set statement (see policy)
    • Must link to publisher version
    • Publisher's version/PDF cannot be used
    • If mandated sooner than 12 months, must obtain waiver from Editors or use AuthorChoice
    • Reviewed on 07/08/2014
  • Classification

Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: The use of stable isotope tags in quantitative peptidomics offers many advantages, but the laborious identification of matching sets of labeled peptide peaks is still a major bottleneck. Here we present labelpepmatch, an R-package for fast and straightforward analysis of LC-MS spectra of labeled peptides. This open-source tool offers fast and accurate identification of peak pairs alongside an appropriate framework for statistical inference on quantitative peptidomics data, based on techniques from other -omics disciplines. A relevant case study on the desert locust Schistocerca gregaria proves our pipeline to be a reliable tool for quick but thorough explorative analyses.
    No preview · Article · Feb 2016 · Journal of Proteome Research
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    ABSTRACT: Glycosylation is an important PTM and is critical for manufacture and efficacy of therapeutic glycoproteins. Glycan significantly influences the biological properties of human follicle-stimulating hormone (hFSH). Using a glycoproteomic strategy, this study compared the glycosylation of a putative highly purified FSH (uhFSH) obtained from human urine with that of a recombinant human FSH (rhFSH) obtained from Chinese hamster ovary (CHO) cells. Intact and subunit masses, N-glycans, N-glycosylation sites, and intact N- and O-glycopeptides were analyzed and compared by mass spectrometry. Classic and complementary analytical methods, including SDS-PAGE, isoelectric focusing, and the Steelman-Pohley bioassay were also employed to compare their intact molecular weights, charge variants, and specific activities. Results showed that highly sialylated, branched, and macro-heterogeneity glycans are predominant in the uhFSH compared with rhFSH. The O-glycopeptides of both hFSHs, which have not been described previously, were characterized herein. A high degree of heterogeneity was observed in the N-glycopeptides of both hFSHs. The differences in glycosylation provide useful information in elucidating and in further investigation of the critical glycan structures of hFSH.
    No preview · Article · Jan 2016 · Journal of Proteome Research
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    ABSTRACT: Indian rhesus macaques are arguably the most reliable animal models in AIDS research. In this species the MHC class I allele Mamu-B*08, among others, is associated with elite control of SIV replication. A similar scenario is observed in humans where the expression of HLA-B*27 or HLA-B*57 has been linked to slow or no progression to AIDS after HIV infection. Despite having large differences in their primary structure, it has been reported that HLA-B*27 and Mamu-B*08 display peptides with sequence similarity. To fine-map the Mamu-B*08 binding motif and assess its similarities with that of HLA-B*27 we affinity purified the peptidomes bound to these MHC class I molecules and analyzed them by LC-MS identifying several thousands of endogenous ligands. Sequence analysis of both sets of peptides revealed a degree of similarity in their binding motifs, especially at peptide position 2 (P2) where arginine was present in the vast majority of ligands of both allotypes. In addition, several differences emerged from this analysis: (i) ligands displayed by Mamu-B*08 tended to be shorter and to have lower molecular weight, (ii) Mamu-B*08 showed a higher preference for glutamine at P2 as a suboptimal binding motif and (iii) the second major anchor position, found at PΩ, was much more restrictive in Mamu-B*08. In this regard, HLA-B*27 bound efficiently peptides with aliphatic, aromatic (including tyrosine) and basic C-terminal residues while Mamu-B*08 preferred peptides with leucine and phenylalanine in this position. Finally, in silico estimations of binding efficiency and competitive binding assays to Mamu-B*08 of several selected peptides revealed a good correlation between the characterized anchor motif and binding affinity. These results deepen our understanding of the molecular basis of the presentation of peptides by Mamu-B*08 and can contribute to the detection of novel SIV epitopes restricted by this allotype.
    No preview · Article · Jan 2016 · Journal of Proteome Research
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    ABSTRACT: We describe a novel Solid-phase Reversible Sample-Prep (SRS) platform, which enables rapid sample preparation for concurrent proteome and N-glycome characterization for nearly all protein samples. SRS utilizes a uniquely functionalized, silica-based bead that has strong affinity toward proteins with minimal-to-no affinity for peptides and other small molecules. By leveraging this inherent size difference between proteins and peptides, SRS permits high-capacity binding of proteins, rapid removal of small molecules (detergents, metabolites, salts, peptides, etc.), extensive manipulation including enzymatic and chemical treatments on beads-bound proteins, and easy recovery of N-glycans and peptides. SRS was evaluated in a wide range of samples including glycoproteins, cell lysate, murine tissues, and human urine. SRS was also coupled with a quantitative strategy to investigate the differences between DU145 prostate cancer cells and its DIAPH3-silenced counterpart. Previous studies suggested that DIAPH3 silencing in DU145 induced transition to an amoeboid phenotype that correlated with tumor progression and metastasis. In this pilot study we identified distinct proteomic and N-glycomic alterations between them. A metastasis-associated tyrosine kinase receptor ephrin-type-A receptor (EPHA2) was highly up-regulated in DIAPH3-silenced cells, indicating possible connection between EPHA2 and DIAPH3. Moreover, distinct alterations in the N-glycome were identified, suggesting cross-links between DIAPH3 and glycosyltransferase networks.
    No preview · Article · Jan 2016 · Journal of Proteome Research
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    ABSTRACT: Due to the clinical significance of carotid atherosclerosis, the search for novel biomarkers has become a priority. The aim of the present study was to compare the protein secretion profile of the carotid atherosclerotic plaque (CAP, n=12) and non-atherosclerotic mammary artery (MA, n=10) secretomes. We used a non-targeted proteomic approach which incorporated tandem immunoaffinity depletion, iTRAQ labelling, and nanoflow liquid chromatography coupled to high-resolution mass spectrometry. In total, 162 proteins were quantified, of which 25 showed statistically significant differences in secretome levels between carotid atherosclerotic plaque and non-diseased mammary artery. We found increased levels of neutrophil defensin 1, apolipoprotein E, clusterin and zinc-alpha-2-glycoprotein in CAP secretomes. Results were validated by ELISA assays. Also, differentially secreted proteins are involved in pathways such as focal adhesion and leukocyte transendothelial migration. In conclusion, this study provides a subset of identified proteins that are differently expressed in secretomes of clinical significance.
    No preview · Article · Jan 2016 · Journal of Proteome Research
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    ABSTRACT: Staphylococcus aureus resistance to antibiotics is a significant clinical problem worldwide. In this study, an untargeted lipidomics approach was used to compare the lipid fingerprints of S. aureus clinical isolates that are resistant and sensitive to antibiotics. High-performance liquid chromatography coupled with time-of-flight mass spectrometry was employed to rapidly and comprehensively analyze bacterial lipids. Chemometric and statistical analyses of the obtained lipid fingerprints revealed variations in several lipid groups between S. aureus strains resistant and sensitive to tested antibiotics, including methicillin, gentamicin, ciprofloxacin, erythromycin and fusidic acid. The levels of identified monoglycosyldiacylglycerol, phosphatidylglycerol and diglycosyldiacylglycerol lipid groups were found to be upregulated in antibiotic-resistant S. aureus strains, whereas the levels of diacylglycerol lipid groups were downregulated. Differences in the lipid patterns between sensitive and resistant S. aureus strains suggest that antibiotic susceptibility may be associated with the lipid composition of bacterial cells. The lipids that were found to significantly differ between antibiotic-resistant and antibiotic-sensitive clinical isolates are involved in the biosynthesis of major S. aureus membrane lipids and lipoteichoic acid. This study indicates that S. aureus lipid biosynthesis pathways should be explored further to better understand the mechanism of antibiotic resistance in S. aureus strains.
    No preview · Article · Jan 2016 · Journal of Proteome Research
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    ABSTRACT: The destruction of articular cartilage in osteoarthritis involves chondrocyte dysfunction and imbalanced extracellular matrix (ECM) homeostasis. Pro-inflammatory cytokines such as interleukin-1α (IL-1α) contribute to osteoarthritis pathophysiology, but the effects of IL-1α on chondrocytes within their tissue microenvironment have not been fully evaluated. To redress this we used label-free quantitative proteomics to analyze the chondrocyte response to IL-1α within a native cartilage ECM. Mouse femoral heads were cultured with and without IL-1α and both the tissue proteome and proteins released into the media were analyzed. New elements of the chondrocyte response to IL-1α related to cellular stress included markers for protein misfolding (Armet, Creld2 and Hyou1), enzymes involved in glutathione biosynthesis and regeneration (Gstp1, Gsto1 and Gsr) and oxidative stress proteins (Prdx2, Txn, Atox1, Hmox1 and Vnn1). Other proteins previously not associated with the IL-1α response in cartilage included ECM components (Smoc2, Kera and Crispld1) and cysteine proteases (cathepsin Z and legumain), while chondroadherin and cartilage-derived C-type lectin (Clec3a) were identified as novel products of IL-1α induced cartilage degradation. This first proteome-level view of the cartilage IL-1α response identified candidate biomarkers of cartilage destruction and novel targets for therapeutic intervention in osteoarthritis.
    No preview · Article · Jan 2016 · Journal of Proteome Research
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    ABSTRACT: The illicit drug 3,4-methylenedioxymethamphetamine (MDMA) has profound physiological cerebral, cardiac and hepatic effects that are reflected in the blood. Screening of blood for MDMA and other narcotics are routinely performed in forensics analysis using ultra-performance liquid chromatography with high-resolution time-of-flight mass spectrometry (UPLC-HR-TOFMS). The aim of this study was to investigate whether such UPLC-HR-TOFMS data collected over a two year period could be used for untargeted metabolomics to determine MDMA metabolites as well as endogenous changes related to drug response and toxicology. Whole blood samples from living Danish drivers' positive for MDMA in different concentrations were compared to negative control samples using various statistical methods. The untargeted identification of known MDMA metabolites was used to validate the methods. The results further revealed changes of several acylcarnitines, adenosine monophosphate (AMP), adenosine, inosine, thiomorpholine 3-carboxylate (TMC), tryptophan, S-adenosyl-L-homocysteine (SAH) and lysophospatidylcholine (lysoPC) species in response to MDMA. These endogenous metabolites could be implicated in an increased energy demand and mechanisms related to the serotonergic syndrome as well as drug induced neurotoxicity. The findings showed that it was possible to extract meaningful results from retrospective UPLC-HR-TOFMS screening data for metabolic profiling in relation to drug metabolism, endogenous physiological effects, and toxicology.
    No preview · Article · Dec 2015 · Journal of Proteome Research
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    ABSTRACT: The filamentous fungus Trichoderma reesei is used for industrial production of secreted enzymes including carbohydrate active enzymes, such as cellulases and hemicellulases. Production of many of these enzymes by T. reesei is influenced by the carbon source it grows on, where the regulation system controlling hydrolase genes involves various signaling pathways. T. reesei was cultivated in the presence of sorbitol, a carbon source that does not induce production of cellulases and hemicellulases, and then exposed to either sophorose or spent grain extract which are efficient inducers of the enzyme production. Specific changes at phosphorylation sites were investigated in relation to the production of cellulases and hemicellulases using a MS-based framework. Proteome-wide phosphorylation following carbon source exchange was investigated at early stages of induction: 0, 2, 5, and 10 minutes. The workflow involved sequential trypsin digestion, TiO2 enrichment, and MS analysis using a Q Exactive mass spectrometer. We report on the identification and quantitation of 1721 phosphorylation sites. Investigation of the data revealed a complex signaling network activated upon induction involving components related to light-mediated cellulase induction, osmoregulation, and carbon sensing. Changes in protein phosphorylation were detected in the glycolytic pathway, suggesting an inhibition of glucose catabolism at 10 minutes after addition of sophorose and as early as 2 minutes after addition of spent grain extract. Differential phosphorylation of factors related to carbon storage, intracellular trafficking, cytoskeleton and cellulase gene regulation were also observed.
    No preview · Article · Dec 2015 · Journal of Proteome Research
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    ABSTRACT: In order to obtain more information about human proteome, especially about proteoforms (protein species) coded by 18th chromosome, proteins from human cancer cell line (HepG2) were separated by two-dimensional gel electrophoresis (2DE). Initially, proteins in major spots were identified. According to parameters (pI/Mw) of identified proteins the gel was calibrated. Using this calibrated gel, a virtual two-dimensional (2D) map of proteoforms coded by chromosome 18 was constructed. Next, the produced gel was divided into 96 sections with determined coordinates. Each section was cut, shredded, and treated by trypsin according to mass-spectrometry protocol. After protein identification by shotgun mass-spectrometry using LC ESI-MS/MS, a list of 22771 proteoforms (product of 3789 genes) was generated. Among them, 176 proteoforms are representing 39 genes of 18th chromosome. The 3D-graphs showing distribution of different proteoforms from the same gene in 2D map were generated. This is a first step in creation of 2DE-based knowledge database of proteins coded by 18th chromosome.
    No preview · Article · Dec 2015 · Journal of Proteome Research