Proteomics Journal Impact Factor & Information

Publisher: Wiley-VCH Verlag

Journal description

Proteomics is intended to become the premier international source for information in the field of proteomics. Its mission is to integrate the various areas of this rapidly developing field including methodological developments in protein separation and characterisation advances in bioinformatics and novel applications of proteomics in all areas of the life sciences and industry. An explosive growth in proteomics is predicted for the post-genomic era and Proteomics will be the journal in which to disseminate the results of these endeavours giving new insights into protein functions interactions and pathways. Proteomics publishes several special issues per year each of which is devoted to a hot topic in the field.

Current impact factor: 3.81

Impact Factor Rankings

2015 Impact Factor Available summer 2016
2014 Impact Factor 3.807
2013 Impact Factor 3.973
2012 Impact Factor 4.132
2011 Impact Factor 4.505
2010 Impact Factor 4.815
2009 Impact Factor 4.426
2008 Impact Factor 4.586
2007 Impact Factor 5.479
2006 Impact Factor 5.735
2005 Impact Factor 6.088
2004 Impact Factor 5.483
2003 Impact Factor 5.766
2002 Impact Factor 4.007

Impact factor over time

Impact factor

Additional details

5-year impact 3.82
Cited half-life 6.30
Immediacy index 0.79
Eigenfactor 0.03
Article influence 1.09
Website Proteomics website
Other titles Proteomics (Online), Proteomics
ISSN 1615-9861
OCLC 47059548
Material type Document, Periodical, Internet resource
Document type Internet Resource, Computer File, Journal / Magazine / Newspaper

Publisher details

Wiley-VCH Verlag

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  • Classification

Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Proteomic exploration of the effects of psychotropic drugs on specific brain areas in rodents has the potential to uncover novel molecular networks and pathways affected by psychotropic medications, and may inform etiologic hypotheses on mental disorders. Haloperidol, a widely used first-generation antipsychotic, has been shown to produce structural and functional changes of the hippocampus, a brain region also implicated in the neuropathology of disorders such as schizophrenia and bipolar disorder. Seven adult male C57BL/6 mice were injected daily intraperitoneally with 0.5 mg/kg of haloperidol, for 28 days. A control group of six animals was injected with vehicle only (saline). Protein levels of post-mortem hippocampus homogenate were determined using label-free liquid chromatography/tandem mass spectrometry (LC/MS/MS). In the treatment group, 216 differentially expressed hippocampal proteins were identified as compared to controls. Ingenuity Pathway Analysis (IPA) implicated oxidative phosphorylation and mitochondrial function as top canonical pathways, and local networks involved in tubulin-mediated cytoskeleton dynamics, clathrin-mediated endocytosis, and extracellular signal-regulated kinase (ERK) - and c-Jun N-terminal kinase (JNK) signaling. The findings of this study could stimulate further research into the cellular mechanisms associated with haloperidol treatment and the pathophysiology of psychotic disorders, assisting treatment biomarker discovery. Data are available via ProteomeXchange with identifier PXD002250. This article is protected by copyright. All rights reserved.
    Proteomics 11/2015; DOI:10.1002/pmic.201500242
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    ABSTRACT: Phosphorus is an essential macronutrient for plant growth and development. Plants can respond defensively to phosphorus deficiency by modifying their morphology and metabolic pathways via the differential expression of low Pi-responsive genes. To better understand the mechanisms by which the Masson pine (Pinus massoniana) adapts to phosphorus deficiency, we conducted comparative proteomic analysis using an elite line exhibiting high tolerance to phosphorus deficiency. The selected seedlings were treated with 0.5 mM KH2 PO4 (control), 0.01 mM KH2 PO4 (P1) or 0.06 mM KH2 PO4 (P2) for 48 days. Total protein samples were separated via two-dimensional gel electrophoresis (2DE). A total of 98 differentially expressed proteins, which displayed at least 1.7-fold change expression compared to the control levels (p ≤ 0.05), were identified by MALDI-TOF/TOF mass spectrometry. These Pi starvation-responsive proteins were implicated in photosynthesis, defense, cellular organization, biosynthesis, energy metabolism, secondary metabolism, signal transduction etc. Therefore, these proteins might play important roles in facilitating internal phosphorus homeostasis. Additionally, the obtained data may be useful for the further characterization of gene function and may provide a foundation for a more comprehensive understanding of the adaptations of the Masson pine to phosphorus-deficient conditions. This article is protected by copyright. All rights reserved.
    Proteomics 11/2015; DOI:10.1002/pmic.201500140
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    ABSTRACT: Secreted cytokines and growth factors play a key role in the modulation of stem cell proliferation, differentiation and survival. To investigate the interplay between the changes in their expression levels, we used the newly characterised human amniotic fluid derived-mesenchymal progenitor MePR-2B cell line differentiated to a neuro-glial phenotype and exploited the very high sensitivity and versatility of magnetic beads-based immunoassays. We found that a sub-set of proteins, including the cytokines IL-6, TNFα, IL-15, IFNγ, IL-8, IL-1ra, MCP-1/CCL2, RANTES and the growth factor PDGFbb, underwent a significant down-regulation following neuro-glial differentiation, whereas the expression levels of IL-12 p70, IL-5, IL-7, bFGF, VEGF and G-CSF were increased. The role of MCP-1/CCL2, previously identified as a regulator of neural progenitor stem cell differentiation, has been further investigated at transcriptional level, revealing that both the chemokine and its receptor are co-expressed in MePR-2B cells and that are regulated upon differentiation, suggesting the presence of an autocrine and paracrine loop in differentiating cells. Moreover, we demonstrated that exogenous CCL2 is capable to affect neuro-glial differentiation in MePR-2B cells, thus providing novel evidences for the potential involvement of chemokine-mediated signaling in progenitor/stem cells differentiation processes and fate specification. This article is protected by copyright. All rights reserved.
    Proteomics 11/2015; DOI:10.1002/pmic.201500223
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    ABSTRACT: Plant cell walls contain a large proportion of polysaccharides (90-95% of cell wall mass) and proteins (5-10%) which play major roles in cell wall plasticity during development and in response to environmental cues. Here we present cell wall proteomics data of Arabidopsis thaliana roots. Plants were cultivated in hydroponic conditions. Cell wall protein extracts were prepared and analyzed in two different ways in order to enlarge the coverage of the root cell wall proteome: proteins were analyzed either directly or following an affinity chromatography on a combinatorial peptide ligand library (CPLL) to reduce the concentration dynamic range. Proteins were identified by LC-MS/MS and bioinformatics. Altogether, 424 proteins having predicted signal peptides have been identified (CWPs). CPLL permitted to identify low abundant CWPs never described before, thus enlarging the coverage of the root cell wall proteome. The number of oxido-reductases is particularly high and includes a large collection of class III peroxidases (CIII Prxs) (38 out of the 73 A. thaliana CIII Prxs). For the first time, hydroxyproline (Hyp) residues were localized at conserved positions in CIII Prx amino acid sequences. This article is protected by copyright. All rights reserved.
    Proteomics 11/2015; DOI:10.1002/pmic.201500129
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    ABSTRACT: We have applied a serologic proteomic workflow involving three complementary MS approaches to a tissue-specific Kras(G12D) -knockin mouse model of pancreatic cancer that consistently forms pre-cancerous lesions by four months of age. The three proteomics applications were highly complementary and allowed us to survey the entire range of low to high molecular weight serologic proteins. Combined, we identified 121 (49↓, 72↑) unique and statistically relevant serologic biomarkers with 88% previously reported to be associated with cancer and 38% specifically correlated with pancreatic cancer. Four markers, lysozyme C2, cytokeratin 19, Serpina1A, and Pcf11, were further verified by Western blotting. When applying systems analysis, the top associated gene ontology functions were tied to wound healing, RXR signaling, growth, differentiation, and innate immune activation through the JAK/STAT pathway. Upon further investigation of the apparent immune response using a multiplex cytokine screen, we found that IFN-γ, VEGF, and GM-CSF were significantly increased in serum from the Kras(G12D) animals compared to littermate controls. By combining three complementary MS applications, we were able to survey the native intact peptidome and the global proteome in parallel, unveiling pathways that may be biologically relevant to promotion of pancreatic cancer progression and serologic markers of non-invasive early-stage neoplasia. This article is protected by copyright. All rights reserved.
    Proteomics 11/2015; DOI:10.1002/pmic.201500133
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    ABSTRACT: In mass-spectrometry based quantitative proteomics, the false discovery rate control (i.e. the limitation of the number of proteins which are wrongly claimed as differentially abundant between several conditions) is a major post-analysis step. It is classically achieved thanks to a specific statistical procedure which computes the adjusted p-values of the putative differentially abundant proteins. Unfortunately, such adjustment is conservative only if the p-values are well-calibrated; the false discovery control being spuriously underestimated otherwise. However, well-calibration is a property that can be violated in some practical cases. To overcome this limitation, we propose a graphical method to straightforwardly and visually assess the p-value well-calibration, as well as the R codes to embed it in any pipeline.
    Proteomics 11/2015; DOI:10.1002/pmic.201500189
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    ABSTRACT: Eggs are the rarest cell in the human body, yet their study is essential for the fields of fertility, reproduction, and fetal health. Guo et al use a "surrogate" animal to discover the phosphoproteomic pathways involved in egg activation. With datasets of several thousand phosphosites on 2500 different proteins, these investigators have defined new pathways, connections to pathways, and priorities in searches for how eggs are activated at fertilization. These results in a sea urchin are now transposable to mammals for testing on a per candidate strategy. This article is protected by copyright. All rights reserved.
    Proteomics 11/2015; DOI:10.1002/pmic.201500426
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    ABSTRACT: Arginine methylation on non-histone proteins is associated with a number of cellular processes including RNA splicing, protein localisation and the formation of protein complexes. In this manuscript, Saccharomyces cerevisiae proteome arrays carrying 4,228 proteins were used with an anti-methylarginine antibody to first identify 88 putatively arginine-methylated proteins. By treating the arrays with recombinant arginine methyltransferase Hmt1, 42 proteins were found to be possible substrates of this enzyme. Analysis of the putative arginine-methylated proteins revealed that they were predominantly nuclear or nucleolar in localisation, consistent with the localisation of Hmt1. Many are involved in known methylarginine-associated functions, such as RNA processing and ribonucleoprotein complex biogenesis, yet others are of newer classes, namely RNA/DNA helicases and tRNA-associated proteins. Using ex vivo methylation and tandem mass spectrometry, a set of 12 proteins (Brr1, Dia 4, Hts1, Mpp10, Mrd1, Nug1, Prp43, Rpa43, Rrp43, Spp381, Utp4 and Npl3), including the RNA helicase Prp43 and tRNA ligases Dia 4 and Hts1, were all validated as Hmt1 substrates. Interestingly, the majority of these also had human orthologs, or family members, that have been documented elsewhere to carry arginine-methylation. These results confirm arginine methylation as a widespread modification and Hmt1 as the major arginine methyltransferase in the S. cerevisiae cell. This article is protected by copyright. All rights reserved.
    Proteomics 11/2015; DOI:10.1002/pmic.201400564
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    ABSTRACT: Elevated serum retinol binding protein (RBP) concentration has been implicated in the development of insulin resistance and type 2 diabetes. Two series of small molecules have been designed to lower serum levels by reducing secretion of the transthyretin-RBP complex from the liver and enhancing RBP clearance through the kidney. These small molecules were seen to improve glucose and insulin tolerance tests and to reduce body weight gain in mice rendered diabetic through a high fat diet. A proteomics study was conducted to better understand the effects of these compounds in muscle cells, muscle being the primary site for energy expenditure. One lead compound, RTC-15, is seen to have a significant effect on proteins involved in fat and glucose metabolism. This could indicate that the compound is having a direct effect on muscle tissue to improve energy homeostasis as well as a whole body effect on circulating RBP levels. This newly characterised group of anti-diabetic compounds may prove useful in the treatment and prevention of insulin resistance and obesity. This article is protected by copyright. All rights reserved.
    Proteomics 11/2015; DOI:10.1002/pmic.201500050
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    ABSTRACT: Legumes are the major sources of food and fodder with strong commercial relevance, and are essential components of agricultural ecosystems owing to their ability to carry out endosymbiotic nitrogen fixation. In recent years, legumes have become one of the major choices of plant research. The legume proteomics is currently represented by more than 100 reference maps and an equal number of stress-responsive proteomes. Among the 48 legumes in the protein databases, most proteomic studies have been accomplished in two model legumes, soybean and barrel medic. This review highlights recent contributions in the field of legume proteomics to comprehend the defence and regulatory mechanisms during development and adaptation to climatic changes. Here, we attempted to provide a concise overview of the progress in legume proteomics and discuss future developments in three broad perspectives: (i) proteome of organs/ tissues; (ii) subcellular compartments; and (iii) spatiotemporal changes in response to stress. Such data mining may aid in discovering potential biomarkers for plant growth, in general, apart from essential components involved in stress tolerance. The prospect of integrating proteome data with genome information from legumes will provide exciting opportunities for plant biologists towards achievement of long-term goals of crop improvement and sustainable agriculture. This article is protected by copyright. All rights reserved.
    Proteomics 11/2015; DOI:10.1002/pmic.201500257
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    ABSTRACT: Aberrant telomerase reactivation in differentiated cells represents a major event in oncogenic transformation. Recurrent somatic mutations in the human telomerase reverse transcriptase (TERT) promoter region, predominantly localized to two nucleotide positions, are highly prevalent in many cancer types. Both mutations create novel consensus E26 transformation-specific (ETS) motifs and are associated with increased TERT expression. Here, we perform an unbiased proteome-wide survey of transcription factor binding at TERT promoter mutations in melanoma. We observe ELF1 binding at both mutations in vitro and we show that increased recruitment of GABP is enabled by the spatial architecture of native and novel ETS motifs in the TERT promoter region. We characterize the dynamics of competitive binding between ELF1 and GABP and provide evidence for ELF1 exclusion by transcriptionally active GABP. This study thus provides an important description of proteome-wide, mutation-specific binding at the recurrent, oncogenic TERT promoter mutations. This article is protected by copyright. All rights reserved.
    Proteomics 11/2015; DOI:10.1002/pmic.201500327
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    ABSTRACT: Head and neck cancers, including oral squamous cell carcinoma (OSCC), are the sixth most common malignancy in the world and are characterized by poor prognosis and a low survival rate. Saliva is oral fluid with intimate contact with OSCC. Besides non-invasive, simple, and rapid to collect, saliva is a potential source of biomarkers. In this study, we build an SRM assay that targets fourteen OSCC candidate biomarker proteins, which were evaluated in a set of clinically-derived saliva samples. Using Skyline software package, we demonstrated a statistically significant higher abundance of the C1R, LCN2, SLPI, FAM49B, TAGLN2, CFB, C3, C4B, LRG1, SERPINA1 candidate biomarkers in the saliva of OSCC patients. Furthermore, our study also demonstrated that CFB, C3, C4B, SERPINA1 and LRG1 are associated with the risk of developing OSCC. Overall, this study successfully used targeted proteomics to measure in saliva a panel of biomarker candidates for OSCC. This article is protected by copyright. All rights reserved.
    Proteomics 11/2015; DOI:10.1002/pmic.201500224
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    ABSTRACT: Proteomics studies typically analyze proteins at a population level, using extracts prepared from tens of thousands to millions of cells. The resulting measurements correspond to average values across the cell population and can mask considerable variation in protein expression and function between individual cells or organisms. Here, we report the development of micro-proteomics for the analysis of C. elegans, a eukaryote composed of 959 somatic cells and ∼1,500 germ cells, measuring the worm proteome at a single organism level to a depth of ∼ 3,000 proteins. This includes detection of proteins across a wide dynamic range of expression levels (> 6 orders of magnitude), including many chromatin-associated factors involved in chromosome structure and gene regulation. We apply the micro-proteomics workflow to measure the global proteome response to heat-shock in individual nematodes. This shows variation between individual animals in the magnitude of proteome response following heat-shock, including variable induction of heat-shock proteins. The micro-proteomics pipeline thus facilitates the investigation of stochastic variation in protein expression between individuals within an isogenic population of C. elegans. All data described in this study are available online via the Encyclopedia of Proteome Dynamics (, an open access, searchable database resource. This article is protected by copyright. All rights reserved.
    Proteomics 11/2015; DOI:10.1002/pmic.201500264
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    ABSTRACT: Caspase activation and proteolytic cleavages are the major events in the early stage of apoptosis. Identification of protein substrates cleaved by caspases will reveal the occurrence of the early events in the apoptotic process and may provide potential drug targets for cancer therapy. Although several N-terminal MS-based proteomic approaches have been developed to identify proteolytic cleavages, these methods have their inherent drawbacks. Here we apply a previously developed proteomic approach, protein C-terminal enzymatic labeling (ProC-TEL), to identify caspase cleavage events occurring in the early stage of the apoptosis of a myeloma cell line induced by kinase inhibition. Both previously identified and novel caspase cleavage sites are detected and the reduction of the expression level of several proteins is confirmed biochemically upon kinase inhibition although the current ProC-TEL procedure are not fully optimized to provide peptide identifications comparable to N-terminal labeling approaches. The identified cleaved proteins form a complex interaction network with central hubs determining morphological changes during the apoptosis. Sequence analyses show that some ProC-TEL identified caspase cleavage events are unidentifiable when traditional N-terminomic approaches are utilized. This work demonstrates that ProC-TEL is a complementary approach to the N-terminomics for the identification of proteolytic cleavage events such as caspase cleavages in signaling pathways. This article is protected by copyright. All rights reserved.
    Proteomics 11/2015; DOI:10.1002/pmic.201500356
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    ABSTRACT: Histone posttranslational modifications and histone variants control the epigenetic regulation of gene expression and affect a wide variety of biological processes. A complex pattern of such modifications and variants defines the identity of cells within complex organ systems and can therefore be used to characterize cells at a molecular level. However, their detection and identification in situ has been limited so far due to lack of specificity, selectivity and availability of anti-histone antibodies. Here, we describe a novel MALDI imaging mass spectrometry (MALDI-IMS) based workflow, which enables us to detect and characterize histones by their intact mass and their correlation with cytological properties of the tissue using novel statistical and image analysis tools. The workflow allows us to characterize the in situ distribution of the major histone variants and their modification in the mouse brain. This new analysis tool is particularly useful for the investigation of expression patterns of the linker histone H1 variants for which suitable antibodies are so far not available. This article is protected by copyright. All rights reserved.
    Proteomics 11/2015; DOI:10.1002/pmic.201500345
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    ABSTRACT: The slowing down or stalling of replication forks is commonly known as replication stress and arises from multiple causes such as DNA lesions, nucleotide depletion, RNA-DNA hybrids and oncogene activation. The ataxia telangiectasia and Rad3-related kinase (ATR) plays an essential role in the cellular response to replication stress and inhibition of ATR has emerged as therapeutic strategy for the treatment of cancers that exhibit high levels of replication stress. However, the cellular signaling induced by replication stress and the substrates of ATR have not been systematically investigated. In this study, we employed quantitative mass spectrometry-based proteomics to define the cellular signaling after nucleotide depletion-induced replication stress and replication fork collapse following ATR inhibition. We demonstrate that replication stress results in increased phosphorylation of a subset of proteins, many of which are involved in RNA splicing and transcription, and have previously not been associated with the cellular replication stress response. Furthermore, our data reveal the ATR-dependent phosphorylation following replication stress and discover novel putative ATR target sites on MCM6, TOPBP1, RAD51AP1 and PSMD4. We establish that ATR inhibition rewires cellular signaling networks induced by replication stress and leads to the activation of the ATM-driven double strand break repair signaling. This article is protected by copyright. All rights reserved.
    Proteomics 11/2015; DOI:10.1002/pmic.201500172
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    ABSTRACT: Subcellular localisation is an important aspect of protein function, but the protein composition of many intracellular compartments is poorly characterised. For example, many nuclear bodies are challenging to isolate biochemically and thus remain inaccessible to proteomics. Here we explore covariation in proteomics data as an alternative route to subcellular proteomes. Rather than targeting a structure of interest biochemically we target it by machine learning. This becomes possible by taking data obtained for one organelle and searching it for traces of another organelle. As an extreme example and proof-of-concept we predict mitochondrial proteins based on their covariation in published interphase chromatin data. We detect about ⅓ of the known mitochondrial proteins in our chromatin data, presumably most as contaminants. However, these proteins are not present at random. We show covariation of mitochondrial proteins in chromatin proteomics data. We then exploit this covariation by Multiclassifier Combinatorial Proteomics (MCCP) to define a list of mitochondrial proteins. This list agrees well with different databases on mitochondrial composition. This benchmark test raises the possibility that, in principle, covariation proteomics may also be applicable to structures for which no biochemical isolation procedures are available. This article is protected by copyright. All rights reserved.
    Proteomics 10/2015; DOI:10.1002/pmic.201500267
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    ABSTRACT: Genome engineering experiments used to be lengthy, inefficient and often expensive, preventing a widespread adoption of such experiments for the full assessment of endogenous protein functions. With the revolutionary CRISPR/Cas9 technology, genome engineering became accessible to the broad life sciences community and is now implemented in several research areas. One particular field that can benefit significantly from this evolution is proteomics where a substantial impact on experimental design and general proteome biology can be expected. In this review we describe the main applications of genome engineering in proteomics, including the use of engineered disease models and endogenous epitope tagging. In addition, we provide an overview on current literature and highlight important considerations when launching genome engineering technologies in proteomics workflows. This article is protected by copyright. All rights reserved.
    Proteomics 10/2015; DOI:10.1002/pmic.201500262