Journal of Proteome Research Impact Factor & Information

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

2015 Impact Factor Available summer 2016
2014 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: Collagen IV is the main structural protein that provides a scaffold for assembly of basement membrane proteins. Posttranslational modifications such as hydroxylation of proline and lysine and glycosylation of lysine are essential for the functioning of collagen IV triple-helical molecules. These modifications are highly abundant posing a difficult challenge for in-depth characterization of collagen IV using conventional proteomics approaches. Herein, we implemented an integrated pipeline combining high-resolution mass spectrometry with different fragmentation techniques and an optimized bioinformatics workflow to study posttranslational modifications in mouse collagen IV. We achieved 82% sequence coverage for the α1 chain, mapping 39 glycosylated hydroxylysine, 148 4-hydroxyproline and 7 3 hydroxyproline residues. Further, we employed our pipeline to map the modifications on human collagen IV and achieved 85% sequence coverage for the α1 chain, mapping 35 glycosylated hydroxylysine, 163 4-hydroxyproline and 14 3-hydroxyproline residues. Although lysine glycosylation heterogeneity was observed in both mouse and human, 21 conserved sites were identified. Likewise, 5 3 hydroxyproline residues were conserved between mouse and human, suggesting that these modification sites are important for collagen IV function. Collectively, these are the first comprehensive maps of hydroxylation and glycosylation sites in collagen IV, which lay the foundation for dissecting the key role of these modifications in health and disease.
    Journal of Proteome Research 11/2015; DOI:10.1021/acs.jproteome.5b00767
  • [Show abstract] [Hide abstract]
    ABSTRACT: Standard forensic procedures to examine bullets after an exchange of fire include a mechanical or ballistic reconstruction of the event. While this is routine to identify which projectile hit a subject by DNA analysis of biological material on the surface of the projectile, it is rather difficult to determine which projectile caused the lethal injury - often the crucial point with regard to legal proceedings. With respect to fundamental law it is the duty of the public authority to make every endeavor in order to solve every homicide case. To improve forensic examinations we present a forensic proteomic method to investigate biological material from a projectile's surface and determine the tissues traversed by it. To obtain a range of relevant samples, different major bovine organs were penetrated with projectiles experimentally. After tryptic "on-surface" digestion, mass spectrometry-based proteome analysis and statistical data analysis, we were able to achieve a cross-validated organ classification accuracy of over 99%. Different types of anticipated external variables exhibited no prominent influence on the findings. In addition, shooting experiments were performed to validate the results. Finally, we show that these concepts could be applied to a real case of murder in order to substantially improve the forensic reconstruction.
    Journal of Proteome Research 11/2015; DOI:10.1021/acs.jproteome.5b00704
  • [Show abstract] [Hide abstract]
    ABSTRACT: Emerging evidence implicates ER stress caused by unfolded mutant proteins in chondrocytes as the underlying pathology of chondrodysplasias. ER stress is triggered in hypertrophic chondrocytes (HCs) in a mouse model (13del) of metaphyseal chondrodysplasia type Schmid (MCDS) caused by misfolded mutant collagen X proteins, but the HCs do not undergo apoptosis, rather chondrocyte differentiation is altered causing skeletal abnormality. How 13del HCs can escape from apoptosis and survive ER stress is not understood. Here, we compared the proteomes of HCs isolated from 13del growth plates with normal HCs, using label-free quantitative mass spectrometry approach. Pathway enrichment analyses of differentially expressed proteins showed significant changes in glycolysis and ER-mitochondria pathways in 13del HCs, as well as in ATDC5 cell lines expressing wt and 13del collagen X. In vivo, we showed expression of mitochondrial calcium channels was reduced while mitochondrial membrane polarity was maintained in 13del chondrocytes, while in vitro, glucose uptake was maintained. We propose 13del HCs survive by a mechanism whereby changes in ER-mitochondria communication reduce import of calcium coupled with maintenance of mitochondrial membrane polarity. These findings provide the initial insights to our understanding of growth plate changes caused by protein misfolding in the pathogenesis of chondrodysplasias (Just accepted Manuscript)DOI: DOI: 10.1021/acs.jproteome.5b00537
    Journal of Proteome Research 11/2015;
  • [Show abstract] [Hide abstract]
    ABSTRACT: Mass spectrometry (MS)-based proteomic approaches have largely facilitated our systemic understanding of cellular processes and biological functions. Cutoffs in protein expression fold changes (FC) are often arbitrarily determined in MS-based quantification with no demonstrable determination of small magnitude changes in protein expression. Therefore, many biological insights may remain veiled due to high FC cutoffs. Herein we employ the intestinal epithelial cell (IEC) line Caco-2 as a model system to demonstrate the dynamicity of tandem-mass-tag (TMT) labeling over a range of 5 - 40% changes in protein abundance, with the variance controls of ±5% FC for around 95% of TMT ratios when sampling nine to twelve biological replicates. We further applied this procedure to examine the temporal proteome of Caco-2 cells upon exposure to human whey proteins (WP). Pathway assessments predict subtle effects due to WP in moderating xenobiotic metabolism, promoting proliferation and various other cellular functions in differentiating enterocyte-like Caco-2 cells. This demonstration of a sensitive MS approach may open up new perspectives in the system-wide exploration of elusive or transient biological effects by facilitating scrutiny of narrow windows of proteome abundance changes. Furthermore, we anticipate this study will encourage more investigations of WP on infant gastrointestinal tract development.
    Journal of Proteome Research 11/2015; DOI:10.1021/acs.jproteome.5b00597
  • [Show abstract] [Hide abstract]
    ABSTRACT: Utility of Mini Bronchoalveolar lavage (mBAL) and its applicability in metabolomics has not been explored in the field of human respiratory disease. mBAL "an archetype" of the local lung environment ensures a potent technique to get the snapshot of the epithelial lining fluid afflicted to human lung disorders. Characterization of the mBAL fluid has potential to help in elucidating the composition of the alveoli and airways in the diseased state, yielding diagnostic information of clinical applicability. In this study one of the first attempts has been made to comprehensively assign and detect metabolites in mBAL fluid, extracted from human lungs, by the composite use of 800 MHz one dimensional (1D) and two dimensional (2D) NMR, homonuclear J-resolved, COSY, TOCSY and heteronuclear HSQC correlation methods. A foremost all-inclusive sketch of the 50 metabolites have been corroborated and assigned, which can be a resourceful archive to further lung directed metabolomics, prognosis and diagnosis. Thus NMR based mBALF studies, as proposed in this article, will leverage many more prospective respiratory researches for routine clinical application and proves to be a viable approach to mirror the key predisposing factors contributing to the onset of lung disease.
    Journal of Proteome Research 11/2015; DOI:10.1021/acs.jproteome.5b00919
  • [Show abstract] [Hide abstract]
    ABSTRACT: In our previous work, we showed that electrospray ionization of intact polyclonal kappa and lambda light chains isolated from normal serum generates two distinct, Gaussian-shaped, molecular mass distributions representing the light-chain repertoire. During the analysis of a large (>100) patient sample set, we noticed a low-intensity molecular mass distribution with a mean of approximately 24 250 Da, roughly 800 Da higher than the mean of the typical kappa molecular-mass distribution mean of 23 450 Da. We also observed distinct clones in this region that did not appear to contain any typical post-translational modifications that would account for such a large mass shift. To determine the origin of the high molecular mass clones, we performed de novo bottom-up mass spectrometry on a purified IgM monoclonal light chain that had a calculated molecular mass of 24 275.03 Da. The entire sequence of the monoclonal light chain was determined using multienzyme digestion and de novo sequence-alignment software and was found to belong to the germline allele IGKV2-30. The alignment of kappa germline sequences revealed ten IGKV2 and one IGKV4 sequences that contained additional amino acids in their CDR1 region, creating the high-molecular-mass phenotype. We also performed an alignment of lambda germline sequences, which showed additional amino acids in the CDR2 region, and the FR3 region of functional germline sequences that result in a high-molecular-mass phenotype. The work presented here illustrates the ability of mass spectrometry to provide information on the diversity of light-chain molecular mass phenotypes in circulation, which reflects the germline sequences selected by the immunoglobulin-secreting B-cell population.
    Journal of Proteome Research 11/2015; DOI:10.1021/acs.jproteome.5b00711
  • [Show abstract] [Hide abstract]
    ABSTRACT: In recent years, proteomic data have contributed to genome annotation efforts, most notably in humans and mice, and spawned a field termed "proteogenomics". Yeast, in contrast with higher eukaryotes, has a small genome, which has lent itself to simpler ORF prediction. Despite this, continual advances in mass spectrometry suggest that proteomics should be able to improve genome annotation even in this well-characterized species. Here we applied a proteogenomics workflow to yeast to identify novel protein-coding genes. Specific databases were generated, from intergenic regions of the genome, which were then queried with MS/MS data. This suggested the existence of several putative novel ORFs of <100 codons, one of which we chose to validate. Synthetic peptides, RNA-Seq analysis, and evidence of evolutionary conservation allowed for the unequivocal definition of a new protein of 78 amino acids encoded on chromosome X, which we dub YJR107C-A. It encodes a new type of domain, which ab initio modeling suggests as predominantly α-helical. We show that this gene is nonessential for growth; however, deletion increases sensitivity to osmotic stress. Finally, from the above discovery process, we discuss a generalizable strategy for the identification of short ORFs and small proteins, many of which are likely to be undiscovered.
    Journal of Proteome Research 11/2015; DOI:10.1021/acs.jproteome.5b00734
  • [Show abstract] [Hide abstract]
    ABSTRACT: Glycosylation is one of the most common post-translational modifications in proteins, existing in ∼50% of mammalian proteins. Several research groups have demonstrated that mass spectrometry is an efficient technique for glycopeptide identification; however, this problem is still challenging because of the enormous diversity of glycan structures and the microheterogeneity of glycans. In addition, a glycopeptide may contain multiple glycosylation sites, making the problem complex. Current software tools often fail to identify glycopeptides with multiple glycosylation sites, and hence we present GlycoMID, a graph-based spectral alignment algorithm that can identify glycopeptides with multiple hydroxylysine O-glycosylation sites by tandem mass spectra. GlycoMID was tested on mass spectrometry data sets of the bovine collagen α-(II) chain protein, and experimental results showed that it identified more glycopeptide-spectrum matches than other existing tools, including many glycopeptides with two glycosylation sites.
    Journal of Proteome Research 11/2015; DOI:10.1021/acs.jproteome.5b00299
  • [Show abstract] [Hide abstract]
    ABSTRACT: Although the "missing protein" is a temporary concept in C-HPP, the biological information for their "missing" could be an important clue in evolutionary studies. Here we classified missing-protein-encoding genes into two groups, the genes encoding PE2 proteins (with transcript evidence) and the genes encoding PE3/4 proteins (with no transcript evidence). These missing-protein-encoding genes distribute unevenly among different chromosomes, chromosomal regions, or gene clusters. In the view of evolutionary features, PE3/4 genes tend to be young, spreading at the nonhomology chromosomal regions and evolving at higher rates. Interestingly, there is a higher proportion of singletons in PE3/4 genes than the proportion of singletons in all genes (background) and OTCSGs (organ, tissue, cell type-specific genes). More importantly, most of the paralogous PE3/4 genes belong to the newly duplicated members of the paralogous gene groups, which mainly contribute to special biological functions, such as "smell perception". These functions are heavily restricted into specific type of cells, tissues, or specific developmental stages, acting as the new functional requirements that facilitated the emergence of the missing-protein-encoding genes during evolution. In addition, the criteria for the extremely special physical-chemical proteins were first set up based on the properties of PE2 proteins, and the evolutionary characteristics of those proteins were explored. Overall, the evolutionary analyses of missing-protein-encoding genes are expected to be highly instructive for proteomics and functional studies in the future.
    Journal of Proteome Research 11/2015; DOI:10.1021/acs.jproteome.5b00450
  • [Show abstract] [Hide abstract]
    ABSTRACT: Recently, we have developed a quantitative shotgun proteomics strategy called MAPA (mass accuracy precursor alignment). The MAPA algorithm uses high mass accuracy to bin mass-tocharge- ratios (m/z) of precursor ions from LC-MS analyses, determine their intensities and to extract a quantitative sample versus m/z-ratio data alignment matrix from a multitude of samples. Here, we introduce a novel feature of this algorithm by allowing the extraction and alignment of proteotypic peptide precursor ions or any other target peptide from complex shotgun proteomics data for accurate quantification of unique proteins. This strategy circumvents the problem of confusing the quantification of proteins due to undistinguishable protein isoforms by a typical shotgun proteomics approach. We applied this strategy to a comparison of control and heat-treated tomato pollen grains at two developmental stages (post meiotic and mature). Pollen is a temperature-sensitive tissue involved in the reproductive cycle of plants and plays a major role for fruit setting and yield. By LC-MS based shotgun proteomics we identified more than 2000 proteins in total for all different tissues. By applying the targeted MAPA data processing strategy, 51 unique proteins were identified which present heat treatment responsive protein candidates. The potential function of the identified candidates in a specific developmental stage is discussed.
    Journal of Proteome Research 09/2015; DOI:10.1021/pr501240n