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

  • Pre-print
    • Author cannot archive a pre-print version
  • Post-print
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  • Restrictions
    • Upon funder agreement with publisher
  • Conditions
    • Pre-print may be deposited on personal intranet or institutional intranet repository, but not on a public repository
    • Pre-print must not updates with future versions
    • Published source must be acknowledged with set phrases (See policy)
    • Must link to publisher's site:
    • Publisher's version/PDF cannot be used
    • Some journal exceptions-check individual homepages
  • Classification
    ​ white

Publications in this journal

  • Sameh Magdeldin · Yoshitoshi Hirao · Amr Elguoshy · Bo · Ying Zhang · Hidehiko Fujinaka · Keiko Yamamoto · John R Yates · Tadashi Yamamoto
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    ABSTRACT: Urine has evolved as one of the most important biofluids in clinical proteomics due to its non-invasive sampling and its stability. Yet, it is used in clinical diagnostics of several disorders by detecting changes in its components including urinary protein/polypeptide profile. Despite the fact that majority of proteins detected in urine are primarily originated from the urogenital tract, determining its precise source within the urogenital tract remains elusive. In this article, we performed a comprehensive analysis of ureter proteome to assemble the first unbiased ureter dataset. Next, we compared these data to urine, urinary exosome, and kidney mass spectrometric datasets. Our result concluded that among 2217 non redundant ureter proteins, 751 protein candidates (33.8%) were detected in urine as urinary protein/polypeptide or exosomal protein. On the other hand, comparing ureter protein hits (48) that are not shown in corresponding databases to urinary bladder and prostate human protein atlas databases pinpointed 21 proteins that might be unique to ureter tissue. In conclusion, this finding offers future perspectives for possible identification of ureter disease-associated biomarkers such as ureter carcinoma. In addition, the ureter proteomic dataset published in this article will provide a valuable resource for researchers working in the field of urology and urine biomarker discovery. This article is protected by copyright. All rights reserved.
    Proteomics 10/2015; DOI:10.1002/pmic.201500214
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    ABSTRACT: Zymoseptoria tritici causes Septoria tritici blotch disease of wheat. To obtain a comprehensive protein dataset of this fungal pathogen, proteomes of Z. tritici growing in nutrient-limiting and rich media and in vivo at a late stage of wheat infection were fractionated by 1D gel or strong cation exchange (SCX) chromatography and analyzed by LC-MS/MS. A total of 5731, 5376 and 3168 Z. tritici proteins were confidently identified from these conditions, respectively. Of these in vitro and in planta proteins, 9% and 11% were predicted to contain signal peptides, respectively. Functional classification analysis revealed the proteins were involved in the various cellular activities. Comparison of three distinct protein expression profiles demonstrates the elevated carbohydrate, lipid and secondary metabolisms, transport, protein processing and energy production specifically in the host environment, in contrast to the enhancement of signaling, defense, replication, transcription and cell division in vitro. The data provide useful targets towards a better understanding of the molecular basis of Z. tritici growth, development, stress response and pathogenicity. This article is protected by copyright. All rights reserved.
    Proteomics 10/2015; DOI:10.1002/pmic.201500168
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    ABSTRACT: Menopause is one of the crucial physiological events during the life of a woman. Transition of menopause status is accompanied by increased risks of various health problems like osteoporosis. Peripheral blood monocytes (PBM) can differentiate into osteoclasts and produce cytokines important for osteoclast activity. With quantitative proteomics LC-nano-ESI-MS(E) , we performed protein expression profiling of PBM in 42 postmenopausal women with discordant bone mineral density (BMD) levels. Traditional comparative analysis showed proteins encoded by 4 genes (LOC654188, PPIA, TAGLN2, YWHAB) and 3 genes (LMNB1, ANXA2P2, ANXA2) were significantly down- and up-regulated, respectively, in extremely low vs. high BMD subjects. To study functionally orchestrating groups of detected proteins in the form of networks, we performed weighted gene co-expression network analysis (WGCNA) and gene set enrichment analysis (GSEA). WGCNA showed that the module including the annexin gene family was most significantly correlated with low BMD, and the lipid-binding related GO terms were enriched in this identified module. GSEA revealed that two significantly enriched gene sets may be involved in postmenopausal BMD variation by regulating pro-inflammatory cytokines activities. To gain more insights into the proteomics data generated, we performed integrative analyses of the datasets available to us at the genome (DNA level), transcriptome (RNA level) and proteome levels jointly. This article is protected by copyright. All rights reserved.
    Proteomics 10/2015; DOI:10.1002/pmic.201500005
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    ABSTRACT: Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with a life expectancy of less than five years post diagnosis for most patients. Poor molecular characterization of IPF has led to insufficient understanding of the pathogenesis of the disease, resulting in lack of effective therapies. In this study, we have integrated a label free LC-MS based approach with systems biology to identify signaling pathways and regulatory nodes within protein interaction networks that govern phenotypic changes that may lead to IPF. Ingenuity Pathway Analysis of proteins modulated in response to bleomycin treatment identified PI3K/Akt and Wnt signaling as the most significant pro-fibrotic pathways. Similar analysis of proteins modulated in response to VEGF-inhibitor (CBO-P11) treatment identified Natural Killer cell signaling and PTEN signaling as the most significant anti-fibrotic pathways. mTOR and ERK were identified to be key mediators of pro- and anti-fibrotic response, where BLM treatment resulted in increased expression and VEGF-inhibitor treatment attenuated expression of mTOR and ERK. Using a BLM mouse model of pulmonary fibrosis and VEGF-inhibitor CBO-P11 as a therapeutic measure, we identified a comprehensive set of signaling pathways and proteins that contribute to the pathogenesis of pulmonary fibrosis that can be targeted for therapy against this fatal disease. This article is protected by copyright. All rights reserved.
    Proteomics 10/2015; DOI:10.1002/pmic.201500171
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    ABSTRACT: Paralytic shellfish toxins (PSTs) are a group of potent neurotoxic alkaloids produced by cyanobacteria and dinoflagellates. The PST biosynthesis gene cluster and several toxin-related proteins have been unveiled in cyanobacteria, yet little is known about dinoflagellates. Here, we compared the protein profiles of a toxin-producing dinoflagellate Alexandrium catenella (ACHK-T) and its non-toxic mutant (ACHK-NT), and characterized differentially displayed proteins using a combination of the iTRAQ-based proteomic approach and the transcriptomic database. Totally 3488 proteins were identified from A. catenella, and proteins involved in carbohydrate, amino acid and energy metabolism were the most abundant. Among them, 185 proteins were differentially displayed: proteins involved in amino acid biosynthesis, protein and carbohydrate metabolism and bioluminescence were more abundant in ACHK-T, while proteins participating in photosynthesis, fatty acid biosynthesis, and the processes occurring in peroxisome displayed higher abundances in ACHK-NT. Seven toxin-related proteins were identified but they varied insignificantly between the two strains. Different carbon and energy utilization strategies were potentially related to the toxin producing ability, and the regulation mechanism of PST biosynthesis was more complex in dinoflagellates. Our study provides the first comprehensive dataset on the dinoflagellate proteome and lays the groundwork for future proteomic study. This article is protected by copyright. All rights reserved.
    Proteomics 09/2015; DOI:10.1002/pmic.201500156
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    ABSTRACT: Over the past decade, considerable progress has been made with respect to the analytical methods for analysis of glycans from biological sources. Regardless of the specific methods that are used, glycan analysis includes isolation, identification, and quantitation. Derivatization is indispensable to increase their identification. Derivatization of glycans can be performed by permethylation or carbodiimide coupling / esterification. By introducing a fluorophore or chromophore at their reducing end, glycans can be separated by electrophoresis or chromatography. The fluorogenically labeled glycans can be quantitated using fluorescent detection. The recently developed approaches using solid-phase such as glycoprotein immobilization for glycan extraction and on-tissue glycan mass spectrometry imaging demonstrate advantages over methods performed in solution. Derivatization of sialic acids is favorably implemented on the solid support using carbodiimide coupling, and the released glycans can be further modified at the reducing end or permethylated for quantitative analysis. In this review, methods for glycan isolation, identification, and quantitation are discussed. This article is protected by copyright. All rights reserved.
    Proteomics 09/2015; DOI:10.1002/pmic.201500266
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    ABSTRACT: Post-translational modifications of proteins are key events in cellular metabolism and physiology regulation. Lysine acetylation is one of the best studied protein modifications in eukaryotes, but, until recently, ignored in bacteria. However, proteomic advances have highlighted the diversity of bacterial lysine-acetylated proteins. The current data support the implication of lysine acetylation in various metabolic pathways, adaptation and virulence. In this review, we present a broad overview of the current knowledge of lysine acetylation in bacteria. We emphasize particularly the significant contribution of proteomics in this field. This article is protected by copyright. All rights reserved.
    Proteomics 09/2015; DOI:10.1002/pmic.201500258
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    ABSTRACT: Little is known about proteomic differences between pluripotent human peripheral blood monocytes (MN) and their terminally-differentiated pulmonary counterparts, alveolar macrophages (AM). To better characterize these cell populations, we performed a label-free shotgun proteomics assessment of matched AM and MN preparations from eight healthy volunteers. With an FDR of less than 0.45%, we identified 1754 proteins within AM and 1445 from MN. Comparison of the two proteomes revealed that 1239 of the proteins found in AM were shared with MN, whereas 206 proteins were uniquely identified in MN and 515 were unique to AM. Molecular and cellular functions, protein classes, development associations and membership in physiological systems and canonical pathways were identified among the detected proteins. Analysis of biologic processes represented by these proteomes indicated that MN were most prominently enriched for proteins involved in cellular movement and immune cell trafficking. In contrast, AM were enriched for proteins involved in protein trafficking, molecular transport, and cellular assembly and organization.. These findings provide a baseline proteomic resource for further studies aimed at better understanding of the functional differences between MN and AM in both health and disease. This article is protected by copyright. All rights reserved.
    Proteomics 09/2015; DOI:10.1002/pmic.201400496
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    ABSTRACT: Microgravity may cause cognition-related changes in the animal nervous system due to the resulting uneven flow of fluids in the body. These changes may restrict the long-term stay of humans in space for various purposes. In this study, a rat tail suspension model (30(o) ) was used to explore the effects of 21 days of prolonged simulated microgravity (SM) on the expression of proteins involved in cognitive functions in the rat hippocampus. SM decreased the content of γ-aminobutyric acid (GABA) and increased the content of glutamate (Glu) in the rat hippocampus. A comparative (18) O-labelled quantitative proteomics strategy was applied to detect the differential expression of synaptic proteins under SM. Fifty-three proteins were found to be differentially expressed under SM. Microgravity induces difficulty in the formation of the SNARE complex due to the down-regulation of vesicle-associated membrane protein 3 (VAMP3) and syntaxin-1A. Synaptic vesicle recycling may also be affected due to the dysregulation of syntaxin-binding protein 5 (tomosyn), rab3A and its effector rim2. Both processes are disturbed, indicating that presynaptic proteins mediate a GABA/Glu imbalance under SM. These findings provide clues for understanding the mechanism of the GABA/Glu equilibrium in the hippocampus induced by microgravity in space and represent steps toward safe space travel. This article is protected by copyright. All rights reserved.
    Proteomics 09/2015; DOI:10.1002/pmic.201500302
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    ABSTRACT: The marine mussel innate immunity provides protection to pathogen invasion and inflammation. In this regard the mussel haemolymph takes a main role in the animal innate response. Despite the importance of this body fluid in determining the physiological condition of the animal, little is known about the molecular mechanisms underlying the cellular and humoral responses. In this work we have applied a mass spectrometry (nanoLC-MS/MS) strategy integrating genomic and transcriptomic data with the aim to: i) identify the main protein functional groups that characterize haemolymph and ii) to map the elements of innate immunity in the marine mussel Mytilus edulis haemolymph proteome. After sample analysis and first protein identification based on MS/MS data comparison, proteins with unknown functions were annotated with blast using public database (nrNCBI) information. Overall 595 haemolymph proteins were identified with high confidence and annotated. These proteins encompass primary cellular metabolic processes: energy production and metabolism of biomolecules, as well as processes related to oxidative stress defence, xenobiotic detoxification, drug metabolism, and immune response. A group of proteins was identified with putative immune effector, receptor and signalling functions in M. edulis. Data are available via ProteomeXchange with identifier PXD001951. This article is protected by copyright. All rights reserved.
    Proteomics 09/2015; DOI:10.1002/pmic.201500118
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    ABSTRACT: Previous studies have reported that lindane, an organochlorine pesticide induces oxidative stress in rat brain that may lead to neurodegeneration. However, as the proteins involved in lindane induced neurodegeneration are yet to be identified, the present study aims to identify the proteins that may regulate lindane induced neurotoxicity. The data showed that repeated exposure of lindane (2.5mg/kg) for 21 days to adult rats significantly increased the reactive oxygen species and lipid peroxidation in different brain regions. Proteomic study revealed that lindane induces major dysregulation in the ubiquitin proteasome pathway. Alterations in the expression of molecular chaperones in brain regions and an increase in the expression of α-synuclein in substantia-nigra and corpus striatum and amyloid precursor protein (APP) in hippocampus and frontal cortex suggests the accumulation of proteins in these brain regions. Western blotting also revealed alterations in the dopaminergic and cholinergic pathways in hippocampus and substantia nigra isolated from lindane treated rats. Neurobehavioral data indicating alterations in learning and working memory, conditioned avoidance response and motor function, supports the proteomic data. The data suggests that repeated exposure of lindane to adult rats induces alterations, which are similar to that seen in neurodegenerative diseases. This article is protected by copyright. All rights reserved.
    Proteomics 09/2015; DOI:10.1002/pmic.201400407
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    ABSTRACT: Tandem MS (MS2) quantification using the series of N- and C-terminal fragment ion pairs generated from isobaric-labelled peptides was recently considered an accurate strategy in quantitative proteomics. However, the presence of multiplexed terminal fragment ion in MS2 spectra may reduce the efficiency of peptide identification, resulting in lower identification scores or even incorrect assignments. To address this issue, we developed a quantitative software tool, denoted isobaric tandem MS quantification (ITMSQ), to improve N- and C-terminal fragment ion pairs based isobaric MS2 quantification. A spectrum splitting module was designed to separate the MS2 spectra from different samples, increasing the accuracy of both identification and quantification. ITMSQ offers a convenient interface through which parameters can be changed along with the labelling method, and the result files and all of the intermediate files can be exported. We performed an analysis of in vivo terminal amino acid labelling (IVTAL) labelled HeLa samples and found that the numbers of quantified proteins and peptides increased by 13.64% and 27.52% after spectrum splitting, respectively. In conclusion, ITMSQ provides an accurate and reliable quantitative solution for N- and C-terminal fragment ion pairs based isobaric MS2 quantitative methods. This article is protected by copyright. All rights reserved.
    Proteomics 09/2015; DOI:10.1002/pmic.201400513
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    ABSTRACT: Enterovirus 71 (EV71) is one of the leading causes of hand, foot and mouth disease with neurological complications in some cases. To study the pathogenesis of EV71 infection, large-scale analyses of EV71 infected cells have been performed. However, most of these studies employed rhabdomyosarcoma (RD) cells or used transcriptomic strategy. Here, we performed SILAC-based quantitative proteomic analysis of EV71-infected U251 cells, a human glioma cell line. A total of 3,125 host proteins were quantified, in which 451 were differentially regulated as a result of EV71 infection at 8 hpi or 20 hpi or both. Gene Ontology analysis indicates the regulated proteins were enriched in "metabolic process", "biological regulation" and "cellular process", implying that these biological processes were affected by EV71 infection. Furthermore, functional study indicated that TRAF2 and TRAF6 among the up-regulated proteins could inhibit the replication of EV71 at the early phase post infection, and the anti-EV71 function of both proteins was independent of interferon β. Our study not only provided an overview of cellular response to EV71 infection in a human glioma cell line, but also found that TRAF2 and TRAF6 might be potential targets to inhibit the replication of EV71. This article is protected by copyright. All rights reserved.
    Proteomics 09/2015; DOI:10.1002/pmic.201500134
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    ABSTRACT: A novel method to achieve highly efficient identification of membrane proteins has been developed based on a covalent binding strategy. For this purpose, magnetic nanoparticles coated with a polyethylene glycol (PEG) layer were synthesized. The PEG chain end was functionalized to form the PEG-tresyl group, which is an octopus-like long arm to capture the free amino groups of membrane proteins. The long arm could be used to bind proteins in a high concentration of the sodium dodecyl sulfate (SDS) medium. Then, the SDS and interfering substances were completely depleted by washing. The covalent binding proteins could form a molecular monolayer on the surface of the nanoparticles in the denatured state, which was significantly favorable for the proteolysis of membrane proteins. Therefore, isolation with covalent binding and highly efficient digestion resulted in a larger scale of membrane proteins. The method has been verified by a proteome identification of mouse liver samples. A total of 2,946 membrane proteins were identified in a membrane protein fraction. A total of 1,505 proteins were characterized as integral membrane proteins, and 735 membrane proteins were identified beyond the largest database summarized by Peptideatlas. This approach has great potential for membrane proteome research.This article is protected by copyright. All rights reserved
    Proteomics 09/2015; DOI:10.1002/pmic.201400572
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    ABSTRACT: Succession is a fundamental concept in ecology, describing the process by which pioneering species colonize a new environmental niche, paving the way for increasingly complex, yet stable ecosystems. The human gut – among the most complex ecosystems known – develops from a nearly sterile state as newborns to a thriving functional network of trillions of organisms living in concert with the host. Recent microbiome analyses have begun to characterize the identities of the microbes during this period of colonization. However, the biochemical processes that govern the stages of inter-organism succession remains a poorly understood, yet exciting frontier. Towards the goal of learning how host-microbe symbiosis arises and is maintained, Young and colleagues (Proteomics 2015, XX, XXXX-XXXX) present a longitudinal metaproteomic case study of an infant during her second and third weeks of life. In the first such analysis of its kind, Young et al. portray overlapping stages of protein production by both the microbiota and the host consistent with their increasing complexity, and deepening interactions.This article is protected by copyright. All rights reserved
    Proteomics 09/2015; DOI:10.1002/pmic.201500359
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    ABSTRACT: The HUPO Brain Proteome Project (HUPO BPP) held its 23rd workshop in São Paulo, Brazil, April 16-17, 2015. The focus of the spring workshop was on strategies and predictive therapies concerning neurodegenerative diseases. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
    Proteomics 09/2015; 15(17):2895-7. DOI:10.1002/pmic.201570154