Proteomics (Proteomics )

Publisher: John Wiley and Sons

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.

  • Impact factor
    4.43
  • 5-year impact
    5.04
  • Cited half-life
    4.00
  • Immediacy index
    0.74
  • Eigenfactor
    0.06
  • Article influence
    1.32
  • 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

John Wiley and Sons

  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
  • Conditions
    • See Wiley-Blackwell entry for articles after February 2007
    • On personal web site or secure external website at authors institution
    • Deposit in institutional repositories is not allowed
    • JASIST authors may deposit in an institutional repository
    • Non-commercial
    • Pre-print must be accompanied with set phrase (see individual journal copyright transfer agreements)
    • Published source must be acknowledged with set phrase (see individual journal copyright transfer agreements)
    • Publisher's version/PDF cannot be used
    • Articles in some journals can be made Open Access on payment of additional charge
    • 'John Wiley and Sons' is an imprint of 'Wiley'
  • Classification
    ​ green

Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Although protein nitration has been reported in the late forties and found to specifically affect tyrosine residues twenty years later, it was not until the early nineties that this posttranslational modification was reported to occur in vivo in mammalian cells. Over the years, this protein modification has increasingly proven to play a major role in a variety of physiological mechanisms through redox signaling and pathological conditions through nitro-oxidative stress, from protozoan parasites to humans. In this issue (Proteomics 2015,15, xxx-yyy), Kang et al. report the identification of the nitroproteome during mating in the yeast Saccharomyces cerevisiae and most interestingly on the changes in nitration induced by the mating signal α-factor of several of these. The correlation of these modifications with the biological functions of these proteins strongly suggest a role for protein nitration in mating signal transduction in yeast, thereby confirming the conservation of this pathway throughout the evolution from unicellular eukaryotes to man. The ubiquity of protein tyrosine nitration whose importance is now also recognized in plants, further highlights its significance as an essential signaling mechanism in eukaryotes. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Proteomics 12/2014;
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    ABSTRACT: Many biologically relevant glycoproteins need to be separated on 1D- or 2D-gels prior to analysis and are available in picomole amounts. Therefore, it is important to have optimized methods to unravel the glycome that combine in-gel digestions with MALDI-TOF-MS. In this technical report, we investigated how the detection of in-gel released N-glycans could be improved by MALDI-TOF-MS. First, an AnchorChip target was tested and compared to ground steel target using several reference oligosaccharides. The highest signals were obtained with an AnchorChip target and D-arabinosazone as the matrix; a limit of detection of 1.3 to 10 fmol was attained. Then, the effect of octyl-β-glucopyranoside, a non-ionic detergent, was studied during in-gel PNGase F digestion of standard glycoproteins and during glycan extraction. Octyl-β-glucopyranoside increased the intensity and the amount of detected neutral as well as acidic N-glycans. A limit of detection of under 7 pmol glycoprotein could be achieved. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Proteomics 12/2014;
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    ABSTRACT: MALDI-TOF profiling of low molecular weight (LMW) peptides (peptidome) usage is limited due to the lack of reproducibility from the confounding inferences of sample preparation, data acquisition and processing. We applied MALDI-TOF analysis to profile urine peptidome with the aims to: 1) compare centrifugal ultrafiltration and dialysis pre-treatments, 2) determine whether using signal LOD (sLOD), together with data normalization, may reduce MALDI-TOF variability. We also investigated the influence of peaks detection on reproducibility. Dialysis allowed to obtain better MALDI-TOF spectra than ultrafiltration. Within the 1000 to 4000 m/z range, we identified 120 and 129 peaks in intra- and inter-assay studies respectively. To estimate the sLOD, serial dilution of pooled urines up to 1/256 were analysed in triplicate. Six data normalization strategies were investigated - the mean, median, internal standard, relative intensity, TIC and linear rescaling normalization. Normalization methods alone performed poorly in reducing features variability while when combined to sLOD adjustment showed an overall reduction in features CVs. Applying a feedback signal processing approach, after median normalization and sLOD adjustment, CVs were reduced from 103% to 26% and 113% to 25% for the intra- and inter-assay respectively, and spectra became more comparable in terms of data dispersion. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Proteomics 12/2014;
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    ABSTRACT: Experimental determination of absolute protein amounts is becoming increasingly important for the establishment and validation of biomarkers, and systems biology approaches aimed at a quantitative description of a biological process. Residing at compartmental or cellular barriers, and acting as prominent drug targets, integral membranes proteins, being completely embedded in the lipid bilayer, possess characteristic physico-chemical properties and are often in low abundance. These features challenge the quantification with targeted mass spectrometry and the ability to accurately determine the amount of membrane proteins with high sensitivity. This review summarizes the current status of targeted membrane protein quantification with emphasis on sample preparation beforehand mass spectrometry. From the beginning to the end of a usual sample preparation workflow, consisting essentially of reference point selection, cell lysis, digestion, and addition of suitable isotope-labelled standards, general and particular challenges for membrane proteins will be discussed step by step. Based on the presentation of current achievements, possible measures to better address these challenges are presented, and future avenues of targeted membrane proteomics. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Proteomics 12/2014;
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    ABSTRACT: Proteases are enzymes that catalyse hydrolysis of peptide bonds thereby controlling the shape, size, function, composition, turnover and degradation of other proteins. In microbes, proteases are often identified as important virulence factors and as such have been targets for novel drug design. It is emerging that some proteases possess additional non-proteolytic functions that play important roles in host epithelia adhesion, tissue invasion, and in modulating immune responses. These additional "moonlighting" functions have the potential to obfuscate data interpretation and have implications for therapeutic design. Moonlighting enzymes comprise a subcategory of multifunctional proteins that possess at least two distinct biological functions on a single polypeptide chain. Presently, identifying moonlighting proteins relies heavily on serendipitous empirical data with clues arising from proteins lacking signal peptides that are localised to the cell surface. Here, we describe examples of microbial proteases with additional non-proteolytic functions, including Streptococcal SpeB, PepO and C5a peptidases, Mycoplasmal aminopeptidases, Mycobacterial chaperones, and viral papain-like proteases. We explore how these non-proteolytic functions contribute to host cell adhesion, modulate the coagulation pathway, assist in non-covalent folding of proteins, participate in cell signalling, and increase substrate repertoire. We conclude by describing how proteomics has aided in moonlighting protein discovery, focusing attention on potential moonlighters in microbial exoproteomes. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Proteomics 12/2014;
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    ABSTRACT: The topic of plant proteomics is reviewed based on related papers published in the journal "Proteomics" since publication of the first issue in 2001. In total, around 300 original papers and 41 reviews published in "Proteomics" between 2000 and 2014 have been surveyed. Our main objective for this review is to help bridge the gap between plant biologists and proteomics technologists, two often very separate groups. Over the past years a number of reviews on plant proteomics have been published [1-7]. To avoid repetition we have focused on more recent literature published after 2010, and have chosen to rather make continuous reference to older publications. The use of the latest proteomics techniques, its integration with other approaches in the Systems Biology direction are discussed more in detail. Finally we comment on the recent history, state of the art, and future directions of plant proteomics, using publications in "Proteomics" to illustrate the progress in the field. The review is organized into two major blocks, the first devoted to provide an overview of experimental systems (plants, plant organs, biological processes) and the second one to the methodology. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Proteomics 12/2014;
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    ABSTRACT: Nutrition is a basic component of life. Nowadays, human nutrition research focusses amongst others on health-related aspects of food ingredients and extracts, and on analyzing the outcomes of specific diets. Usually, food ingredients such as bioactive peptides come in complex matrices. Single compounds, multiple interactions thereof and the underlying food matrix can vary physiological response of the organism. Proteins and peptides derived from food and beverages can cause adverse allergic reactions but are in general required for multiple functions such as growth and homeostatic regulation. Endogenously expressed human proteins and peptides can be used as biomarkers to monitor physiological deregulation and the effects of food consumption. The intestinal microbiome seems to play a fundamental role in establishing and maintaining physiological regulation and in digesting proteins and peptides and other biomolecules derived from food. Notably, the subtle interplay of flavor naturals in food and beverages with olfactory receptors can result in establishing human taste preferences, which again influences overall physiology. This article presents basic approaches and concepts to address scientific questions in nutritional proteomics and discusses potential benefits of proteomics-based methodologies to help advance the field of molecular nutrition research. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Proteomics 12/2014;
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    ABSTRACT: Recent advances in high-throughput experimental techniques have led to an exponential increase in both the size and the complexity of the datasets commonly studied in biology. Data visualisation is increasingly used as the key to unlock this data, going from hypothesis generation to model evaluation and tool implementation. It is becoming more and more the heart of bioinformatics workflows, enabling scientists to reason and communicate more effectively. In parallel, there has been a corresponding trend towards the development of related software, which has triggered the maturation of different visualisation libraries and frameworks. For bioinformaticians, scientific programmers and software developers, the main challenge is to pick out the most fitting one(s) to create clear, meaningful and integrated data visualisation for their particular use cases. In this review, we introduce a collection of open source or free to use libraries and frameworks for creating data visualisation, covering the generation of a wide variety of charts and graphs. We will focus on software written in Java, JavaScript or Python. We truly believe this software offers the potential to turn tedious data into exciting visual stories. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Proteomics 12/2014;
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    ABSTRACT: We present a comprehensive workflow for large scale (>1000 transitions/run) label-free LC-MRM proteome assays. Innovations include automated MRM transition selection, intelligent retention time scheduling (xMRM) that improves Signal/Noise by >2-fold, and automatic peak modeling. Improvements to data analysis include a novel Q/C metric, Normalized Group Area Ratio (NGAR), MLR normalization, weighted regression analysis, and data dissemination through the Yale Protein Expression Database. As a proof of principle we developed a robust 90 minute LC-MRM assay for Mouse/Rat Post-Synaptic Density (PSD) fractions which resulted in the routine quantification of 337 peptides from 112 proteins based on 15 observations per protein. Parallel analyses with stable isotope dilution peptide standards (SIS), demonstrate very high correlation in retention time (1.0) and protein fold change (0.94) between the label-free and SIS analyses. Overall, our first method achieved a technical CV of 11.4% with >97.5% of the 1697 transitions being quantified without user intervention, resulting in a highly efficient, robust, and single injection LC-MRM assay. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Proteomics 12/2014;
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    ABSTRACT: Seminal plasma is a mixture of secretions from several male accessory glands. The seminal plasma contains many secreted proteins which are important for sperm function and male fertility. In the present study, we employed N-linked glycosylated peptide enrichment, combined with liquid chromatography-tandem mass spectrometry analysis, and establish the first large scale N-linked glycoproteome of human seminal plasma. Combined with the results of five biological replicates, a total of 720 N-glycosylated sites on 372 proteins were identified. Analysis of variations among five individuals revealed similar compositions of N-glycosylated proteins in seminal plasma. The N-linked glycoproteome could help us understanding the biological functions of human seminal plasma. The dataset could also be a resource for further screening of biomarkers for male diseases including cancer and infertility at the level of N-glycosylation. For example, N-glycosylated prostate-specific antigen is known to be an efficient biomarker that can distinguish benign prostate hyperplasia from prostate cancer. Data are available via ProteomeXchange with identifier PXD000959. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Proteomics 12/2014;
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    ABSTRACT: The present review highlights the progress made in plant proteomics via the introduction of combinatorial peptide ligand libraries (CPLL) for detecting low-abundance species. Thanks to a novel approach to the CPLL methodology, namely that of performing the capture both under native and denaturing conditions, identifying plant species in the order of thousands, rather than hundreds, is now possible. We report here data on a trio of tropical fruits, namely banana, avocado and mango. The first two are classified as "recalcitrant" tissues since minute amounts of proteins (in the order of 1%) are embedded on a very large matrix of plant-specific material (e.g., polysaccharides and other plant polymers). Yet, even under these adverse conditions we could report, in a single sweep, from 1000 to 3000 unique gene products. In the case of mango the investigation has been extended to the peel too, since this skin is popularly used to flavour dishes in Far East cuisine. Even in this tough peel 330 proteins could be identified, whereas in soft peels, such lemons, one thousand unique species could be detected. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Proteomics 12/2014;
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    ABSTRACT: Pathological levels of oxidative stress (OS) have been implicated in a broad spectrum of diseases. Carbonylation is an irreversible post translational modification that is considered as a universal indicator of OS. The development of new enrichment techniques coupled with the introduction of highly sensitive mass spectrometers has allowed the identification of carbonylated proteins in biological systems. In this study Deng et al.(Proteomics 2015, 15, xxx-yyy) utilized one of these methods to isolate and identify carbonylated proteins that are involved in tetracycline-induced steatosis. They identified 26 proteins that are targets of oxidative stress and most of them were located in the mitochondria. A key carbonylated protein that was identified is long-chain specific acyl-CoA dehydrogenase (ACADL) which has a major role in the β-oxidation of fatty acids. The researchers concluded that tetracycline-induced steatosis is a two-step process which involves lipid overload followed by oxidative stress. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Proteomics 12/2014;
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    ABSTRACT: The plasma proteome remains an attractive biospecimen for mass spectrometry (MS)-based biomarker discovery studies. The success of these efforts relies on the continued development of quantitative MS-based proteomics approaches. Herein we report the use of the SILAC-labeled HepG2 secretome as a source for stable isotope labeled plasma proteins for quantitative LC-MS/MS measurements. The HepG2 liver cancer cell line secretes the major plasma proteins including serum albumin, lipoproteins, proteases inhibitors, coagulation factors, and transporters which represent some of the most abundant proteins in plasma. The SILAC-labeled HepG2 secretome was collected, spiked into human plasma (1:1 total protein), and then processed for LC-MS/MS analysis. A total of 62 and 56 plasma proteins were quantified (heavy:light peptide pairs) from un-depleted and depleted (serum albumin and IgG), respectively with log2 H/L = ±6. Major plasma proteins quantified included albumin, apolipoproteins (e.g., APOA1, APOA2, APOA4, APOB, APOC3, APOE, APOH, and APOM), protease inhibitors (e.g., A2M and SERPINs), coagulation factors (e.g., Factor V, Factor X, fibrinogen), and transport proteins (e.g., TTR). The average log2 H/L values for shared plasma proteins in both un-depleted and depleted plasma samples were 0.43 and 0.44, respectively. This work further expands the SILAC strategy into MS-based biomarker discovery of clinical biospecimens.This article is protected by copyright. All rights reserved
    Proteomics 12/2014;
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    ABSTRACT: Proteomics approaches using mass spectrometry in combination with affinity purification (AP-MS) have emerged as powerful tools to study protein-protein interactions. Here we make use of the specificity of sortase A transpeptidation reaction to prepare affinity matrices in which a protein bait is covalently linked to the matrix via a short C-terminal linker region. As a result of this site-directed immobilization, the bait remains functionally accessible to protein interactions. To apply this approach, we performed SILAC-based pull-down experiments and demonstrate the suitability of the approach.This article is protected by copyright. All rights reserved
    Proteomics 12/2014;
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    ABSTRACT: Many top-down proteomics experiments focus on identifying and localizing post-translational modifications and other potential sources of “mass shift” on a known protein sequence. A simple application to match ion masses and facilitate the iterative hypothesis testing of PTM presence and location would assist with the data analysis in these experiments. ProSight Lite is a free software tool for matching a single candidate sequence against a set of mass spectrometric observations. Fixed or variable modifications, including both post-translational modifications and a select number of glycosylations, can be applied to the amino acid sequence. The application reports multiple scores and a matching fragment list. Fragmentation maps can be exported for publication in either PNG or SVG format. ProSight Lite can be freely downloaded from http://prosightlite.northwestern.edu, installs and updates from the web, and requires Windows 7 or higher.This article is protected by copyright. All rights reserved
    Proteomics 12/2014;
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    ABSTRACT: Total protein approach (TPA) is a proteomic method which allows calculation of concentrations of individual proteins and groups of functionally related proteins in any protein mixture without spike-in standards. Using the two step digestion–filter aided sample preparation method and LC-MS/MS analysis we generated comprehensive quantitative datasets of mouse intestinal mucosa, liver, red muscle fibers, brain, and of human plasma, erythrocytes, and tumor cells lines. We show that the TPA based quantitative data reflect well-defined and specific physiological functions of different organs and cells, for example nutrient absorption and transport in intestine, amino acid catabolism and bile secretion in liver, and contraction of muscle fibers. Focusing on key metabolic processes we compared metabolic capacities in different tissues and cells. In addition, we demonstrate quantitative differences in the mitochondrial proteomes. Providing insight into the abundances of mitochondrial metabolite transporters we demonstrate that their titers are well tuned to cell specific metabolic requirements. This study provides for the first time a comprehensive overview of the protein hardware mediating metabolism in different mammalian organs and cells. The presented approach can be applied to any other system to study biological processes.This article is protected by copyright. All rights reserved
    Proteomics 12/2014;
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    ABSTRACT: The zebrafish owns remarkable regenerative capacities allowing regeneration of several tissues, including the heart, liver and brain. To identify protein dynamics during fin regeneration we used a pulsed SILAC approach that enabled us to detect the incorporation of 13C6-lysine (Lys6) into newly synthesized proteins. Samples were taken at four different time points from non-injured and regrowing fins and incorporation rates were monitored using a combination of single-shot 4 h gradients and high-resolution tandem mass spectrometry. We identified more than 5000 labeled proteins during the first three weeks of fin regeneration and were able to monitor proteins that are responsible for initializing and restoring the shape of these appendages. The comparison of lys-6 incorporation rates between non-injured and regrowing fins enabled us to identify proteins that are directly involved in regeneration. For example, we observed increased incorporation rates of two actinodin family members at the actinotchria, which is a hairlike fibre structure at the tip of regrowing fins. Moreover, we used quantitative real-time RNA measurements of several candidate genes, including osteoglycin, si:ch211–288h17.3, and prostaglandin reductase 1 to correlate the mRNA expression to lys-6 incorporation data. This novel pulsed SILAC methodology in fish can be used as a versatile tool to monitor newly synthesized proteins and will help to characterize protein dynamics during regenerative processes in zebrafish beyond fin regeneration.This article is protected by copyright. All rights reserved
    Proteomics 12/2014;