Proteomics (Proteomics )

Publisher: John Wiley & 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 & 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
    • Not allowed on institutional repository
    • 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-Blackwell'
  • Classification
    ​ green

Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Protein phosphorylation on serine, threonine and tyrosine is known to be involved in a wide variety of cellular processes, signal transduction and bacterial virulence. We characterized, for the first time, the extracellular phosphoproteins of the Pseudomonas aeruginosa PA14 strain. We identified 28 phosphoproteins (59 phosphosites) including enzymes, with various phosphorylation sites, known as potent secreted virulence factors in P. aeruginosa. The high phosphorylation level of these virulence factors might reflect a relationship between Ser/Thr/Tyr phosphorylation and virulence.This article is protected by copyright. All rights reserved
    Proteomics 06/2014;
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    ABSTRACT: Extracellular microvesicles (EVs) are membranous vesicles which are released from diverse cells. These EVs have also been found in a wide range of body fluids. The cargo of EVs, including proteins, lipids, carbohydrates, and nucleic acids can be stably preserved in EVs. Researchers have found that EVs can mediate intercellular communication by shuttling the cargo components. Therefore, EVs can be used for the identification of disease-specific biomarkers. As one class of EVs, urinary exosomes can reflect the status of the renal system. Moreover, urinary exosome analysis can minimize the interference of high abundant proteins in the whole urine sample. Therefore, urinary exosomes have gained much attention in recent years. In this review, we present a comprehensive summary of urinary exosome studies in recent years, including collection, storage, and isolation methods. The normal and disease proteomic analyses of urinary exosomes are also presented. Thus, this review may provide a valuable reference for future research.Extracellular microvesicles (EVs), which are spherical bilayered proteolipids vesicles, can be secreted by a variety of cells with a mean diameter of 20–1,000 nm [1–3]. In recent decades, EVs have gained significant attention as they play important roles in intercellular communication, pathogenesis, drug- and gene-vector delivery, and are possible reservoirs of biomarkers [4]. Urinary EVs have attracted increasing research interest due to their relationship with kidney physiology and disease [5]. This review aims to summarize the progress in urinary EVs isolation methods and proteomic analysis as a reference for future research.This article is protected by copyright. All rights reserved
    Proteomics 06/2014;
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    ABSTRACT: Crosslinking combined with mass spectrometry involves enzymatic digestion of crosslinked proteins and identifying crosslinked peptides. Assignment of crosslinked peptide masses requires a search of all possible binary combinations of peptides from the crosslinked proteins’ sequences, which becomes impractical with increasing complexity of the protein system and/or if digestion enzyme specificity is relaxed. Here we describe an application fast sorting algorithm to search large sequence databases for crosslinked peptide assignments based on mass. This same algorithm has been used previously for assigning disulfide-bridged peptides (Choi, et al., J Prot Res 2010), but has not previously been applied to crosslinking studies.This article is protected by copyright. All rights reserved
    Proteomics 06/2014;
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    ABSTRACT: This study profiled the plasma proteins of patients infected by the 2011 H1N1 influenza virus. Differential protein expression was identified in plasma obtained from non-infected control subjects (n = 15) and H1N1 infected subjects (n = 15). Plasma proteins were separated by a two-dimensional electrophoresis large gel system and identified by nano-ultra performance liquid chromatography-mass spectrometry. Western blot assays were performed to validate proteins. Eight plasma proteins were up-regulated and six proteins were down-regulated among 3316 plasma proteins in the H1N1 infected group as compared with the control group. Of 14 up-and down-regulated proteins, nine plasma proteins were validated by Western blot analysis. Putative protein FAM 157A, leucine rich alpha 2 glycoprotein, serum amyloid A protein, and dual oxidase 1 showed significant differential expression. The identified plasma proteins could be potential candidates for biomarkers of H1N1 influenza viral infection. Further studies are needed to develop these proteins as diagnostic biomarkers.This article is protected by copyright. All rights reserved
    Proteomics 05/2014;
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    ABSTRACT: Arsenic is an environmental pollutant, and its liver toxicity has long been recognized. The effect of arsenic on liver protein expression was analyzed using a proteomic approach in monkeys. Monkeys were orally administered sodium arsenite (SA) for 28 days. As shown by two-dimensional polyacrylamide gel electrophoresis in combination with mass spectrometry, the expression levels of 16 proteins were quantitatively changed in SA-treated monkey livers compared to control-treated monkey livers. Specifically, the levels of two proteins, mortalin and tubulin beta chain, were increased, and 14 were decreased, including plastin-3, cystathionine-beta-synthase, selenium-binding protein 1, annexin A6, alpha-enolase, phosphoenolpyruvate carboxykinase-M, erlin-2, and arginase-1. In view of their functional roles, differential expression of these proteins may contribute to arsenic-induced liver toxicity, including cell death and carcinogenesis. Among the 16 identified proteins, four were selected for validation by western blot and immunohistochemistry. Additional western blot analyses indicated arsenic-induced dysregulation of oxidative stress-, genotoxicity-, and glucose metabolism-related proteins in livers from SA-treated animals. Many changes in the abundance of toxicity-related proteins were also demonstrated in SA-treated human hepatoma cells. These data on the arsenic-induced regulation of proteins with critical roles may help elucidate the specific mechanisms underlying arsenic-induced liver toxicity.This article is protected by copyright. All rights reserved
    Proteomics 05/2014;
  • Proteomics 05/2014; 14(9):973-4.
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    ABSTRACT: Parkinson's disease (PD) is characterized as a movement disorder due to lesions in the basal ganglia. As the major input region of the basal ganglia, striatum plays a vital role in coordinating movements. It receives afferents from the cerebral cortex and projects afferents to the internal segment of the globus pallidus and substantia nigra pars reticulate. Additionally, accumulating evidences support a role for synaptic dysfunction in PD. Therefore, the present study explores the changes in protein abundance involved in synaptic disorders in unilateral lesioned 6-OHDA rat model. Based on 18O/16O labeling technique, striatal proteins were separated using online two-dimensional liquid chromatography (2D-LC), and identified by nano-ESI-Q-TOF. A total of 370 proteins were identified including 76 significantly differentially expressed proteins. Twenty-two down-regulated proteins were found in composition of vesicle, 10 of which were involved in neuronal transmission and recycling across synapses. These include SNARE proteins (SNAP-25, syntaxin-1A, syntaxin-1B, VAMP2), synapsin-1, septin-5, clathrin heavy chain 1, AP-2 complex subunit beta, dynamin-1, and endophilin-A1. Moreover, mass spectrometry result for syntaxin-1A was confirmed by western blot analysis. Overall, these synaptic changes induced by neurotoxin may serve as a reference for understanding the functional mechanism of striatum in PD.This article is protected by copyright. All rights reserved
    Proteomics 05/2014;
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    ABSTRACT: The nucleus is the organelle where basically all DNA-related processes take place in eukaryotes such as replication, transcription and splicing as well as epigenetic regulation. The identification and description of the nuclear proteins is one of the requisites towards a comprehensive understanding of the biological functions accomplished in the nucleus. Many of the regulatory mechanisms of protein functions rely on their post-translational modifications amongst which phosphorylation is probably one of the most important properties affecting enzymatic activity, interaction with other molecules, localization or stability. So far, the nuclear and subnuclear proteome and phosphoproteome of the model plant Arabidopsis thaliana were the objects of very few studies. In this work, we developed a purification protocol of Arabidopsis chromatin-associated proteins and performed proteomic and phosphoproteomic analyses identifying a total of 879 proteins of which 198 were phosphoproteins that were mainly involved in chromatin remodeling, transcriptional regulation and RNA processing. From 230 precisely localized phosphorylation sites (phosphosites), 52 correspond to hitherto unidentified sites. This protocol and data thereby obtained should be a valuable resource for many domains of plant research.This article is protected by copyright. All rights reserved
    Proteomics 05/2014;
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    ABSTRACT: We employ stable isotope labelling and quantitative mass spectrometry to track histone methylation stability. We show that H3 trimethyl K9 and K27 are slow to be established on new histones and slow to disappear from old histones, with half-lives of multiple cell divisions. By contrast the transcription-associated marks K4me3 and K36me3 turn over far more rapidly, with half-lives of 6.8 h and 57 h, respectively. Inhibition of demethylases increases K9 and K36 methylation, with K9 showing the largest and most robust increase. We interpret different turnover rates in light of genome-wide localization data and transcription-dependent nucleosome rearrangements proximal to the transcription start site.This article is protected by copyright. All rights reserved
    Proteomics 05/2014;
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    ABSTRACT: Centromeres are chromosomal regions crucial for correct chromosome segregation during mitosis and meiosis. They are epigenetically defined by centromeric proteins like the centromere-specific histone H3-variant CENP-A. In humans, 16 additional proteins have been described to be constitutively associated with centromeres throughout the cell cycle, known as the constitutive centromere associated network (CCAN). In contrast, only one additional constitutive centromeric protein is known in Drosophila melanogaster (D.mel), the conserved CCAN member CENP-C. To gain further insights into D. melanogaster centromere composition and biology, we analyzed affinity-purified chromatin prepared from D.mel cell lines expressing GFP-tagged H3 variants by mass spectrometry. In addition to already known centromeric proteins, we identified novel factors that were repeatedly enriched in affinity purification-MS experiments. We analyzed the cellular localization of selected candidates by immunocytochemistry and confirmed localization to the centromere and other genomic regions for ten factors. Furthermore, RNAi-mediated depletion of CG2051, CG14480 and Hyd, three of our strongest candidates, leads to elevated mitotic defects. Knockdowns of these candidates neither impair the localization of several known kinetochore proteins nor CENP-ACID loading, suggesting their involvement in alternative pathways that contribute to proper centromere function. In summary, we provide a comprehensive analysis of the proteomic composition of Drosophila centromeres.This article is protected by copyright. All rights reserved
    Proteomics 05/2014;
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    ABSTRACT: The sensor kinase/response regulator system KdpD/KdpE of Escherichia coli regulates the expression of the kdpFABC operon, encoding the high-affinity KdpFABC K+-transport complex. Additionally, it has been suggested that the kdpDE operon itself is subjected to autoregulation by its gene products KdpD and KdpE. However, since kdpFABC- and kdpDE-expression has mainly been studied on the transcriptional level, accurate information on absolute amounts and the stoichiometric subunit composition of KdpFABC and KdpD/KdpE under K+-limiting and K+-non-limiting growth conditions are lacking. In this study we used high sensitive mass spectrometric methods to quantify the amount of subunits of the Kdp(F)ABC complex and KdpD/KdpE. Data-dependent shotgun mass spectrometry was used to assess protein coverage and accessible peptides. Absolute amounts of Kdp(F)ABC and KdpD/KdpE were quantified by targeted MRM analysis in the presence of corresponding heavy labeled standard peptides. Baseline synthesis of Kdp(F)ABC and KdpD/KdpE was found to be in the attomolar range under K+-non-limiting conditions. Under K+−limitation, synthesis of Kdp(F)ABC (KdpA:KdpB:KdpC ratio of 1:1:1) was amplified more than 100-fold, whereas only a 10-fold amplification of KdpD/KdpE (KdpD:KdpE ratio of 1:4) was observed. The results obtained provide a solid basis for follow-up studies on the dynamic regulation of the Kdp system.This article is protected by copyright. All rights reserved
    Proteomics 05/2014;
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    ABSTRACT: Precise protein quantification is essential in comparative proteomics. Currently, quantification bias is inevitable when using proteotypic peptide-based quantitative proteomics strategy for the differences in peptides measurability. To improve quantification accuracy, we proposed an Empirical Rule for Linearly-correlated Peptide Selection (ERLPS) in quantitative proteomics in our previous work. However, a systematic evaluation on general application of ERLPS in quantitative proteomics under diverse experimental conditions needs to be conducted. In this study, the practice workflow of ERLPS was explicitly illustrated, different experimental variables, like different MS system, sample complexities, sample preparations, elution gradients, matrix effects, loading amounts and other factors were comprehensively investigated to evaluate the applicability, reproducibility and transferability of ERPLS. The results demonstrated that ERLPS was highly reproducible and transferable within appropriate loading amounts and linearly correlated response peptides (LRPs) should be selected for each specific experiment. ERLPS was used to proteome samples from yeast to mouse and human, and in quantitative methods from label-free to O18/O16-labeled and SILAC analysis, and enabled accurate measurements for all proteotypic peptide-based quantitative proteomics over a large dynamic range.This article is protected by copyright. All rights reserved
    Proteomics 05/2014;
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    ABSTRACT: Growth and productivity of rice (Oryza sativa L.) are severely affected by salinity. Understanding the mechanisms that protect rice and other important cereal crops from salt stress will help in the development of salt-stress tolerant strains. In this study, rice seedlings of the same genetic species with various salt tolerances were studied. We first used two-dimensional gel electrophoresis (2-DE) to resolve the expressed proteome in rice roots and leaves and then used nanospray liquid chromatography/tandem mass spectrometry (nano-LC/MS/MS) to identify the differentially expressed proteins in rice seedlings after salt treatment. The 2-DE assays revealed that there were 104 differentially expressed protein spots in rice roots and 59 in leaves. Then, we identified 83 proteins in rice roots and 61 proteins in rice leaves by MS analysis. Functional classification analysis revealed that the differentially expressed proteins from roots could be classified into 18 functional categories while those from leaves could be classified into 11 functional categories. The proteins from rice seedlings that most significantly contributed to a protective effect against increased salinity were cysteine synthase, ATP synthase, quercetin 3-O-methyltransferase 1, and lipoxygenase 2. Further analysis demonstrated that the primary mechanisms underlying the ability of rice seedlings to tolerate salt-stress were glycolysis, purine metabolism, and photosynthesis. Thus, we suggest that differentially expressed proteins may serve as marker group for the salt tolerance of rice.This article is protected by copyright. All rights reserved
    Proteomics 05/2014;
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    ABSTRACT: Staphylococcus aureus is one of the major causative agents of severe infections, and is responsible for a high burden of morbidity and mortality. Strains of increased virulence have emerged (e.g., USA300) that can infect healthy individuals in the community and are difficult to treat. To add to the knowledge about the pathophysiology of S. aureus, the adaption to iron restriction, an important in vivo stressor, was studied and the corresponding immune response of the human host characterized.Using a combination of one- and two-dimensional immune proteomics, the human antibody response to the exoproteomes of S. aureus USA300Δspa grown under iron restriction or with excess iron was compared. Human antibody binding to the altered exoproteome under iron restriction showed a 2.7- to 6.2-fold increase in overall signal intensity, and new antibody specificities appeared. Quantification of the secreted bacterial proteins by gel-free proteomics showed the expected strong increase in level of proteins involved in iron acquisition during iron restricted growth compared to iron access. This was accompanied by decreased levels of superantigens and hemolysins. The latter was corroborated by functional PBMC proliferation assays.The present data provide a comprehensive view of S. aureus exoproteome adaptation to iron restriction. Adults have high concentrations of serum antibodies specific for some of the newly induced proteins. We conclude that iron restriction is a common feature of the micro-environment, where S. aureus interacts with the immune system of its human host.This article is protected by copyright. All rights reserved
    Proteomics 05/2014;
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    ABSTRACT: Imaging mass spectrometry (MSI) has emerged as a valuable tool to study the spatial distribution of biomolecules in the brain. Herein MALDI-MSI was used to determine the distribution of endogenous peptides in a rat model of Usher's disease. This rare disease is considered as leading cause of deaf-blindness in humans worldwide. Cryosections of brain tissue were analyzed by MALDI-MSI to differentiate between healthy and diseased rats. MSI results were highly reproducible. Tissue-specific peptides were identified by MS/MS using LC-Orbitrap and MALDI-TOF/TOF analyses. These peptides were proposed for histological classification due to their particular spatial distribution in the brain, e.g. substantia nigra, corpus callosum and hippocampus. Several endogenous peptides showed significantly increased ion densities, particularly in the colliculi superiores and in the substantia nigra of diseased rats including peptides derived from Fsd1, dystrobrevin-β and ProSAAS. Furthermore, several proteolytic degradation products of the myelin basic protein were identified, of which one peptide is most likely mediated by calpain-2. Our findings contribute to the characterization of this animal model and include possible peptide markers of disease.This article is protected by copyright. All rights reserved
    Proteomics 05/2014;
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    ABSTRACT: Imbalance in protein homeostasis in specific subcellular organelles is alleviated through organelle-specific stress response pathways. As a canonical example of stress activated pathway, accumulation of misfolded proteins in Endoplasmic Reticulum (ER) activate unfolded protein response (UPR) in almost all eukaryotic organisms. However, very little is known about the involvement of proteins of other organelles that help to maintain the cellular protein homeostasis during ER stress. In this study, using iTRAQ based LC-MS approach, we identified organelle enriched proteins that are differentially expressed in yeast (Saccharomyces cerevisiae) during ER stress in the absence of UPR sensor IRE1. We have identified about 750 proteins from enriched organelle fraction in three independent iTRAQ experiments. Induction of ER stress resulted in the differentialexpression of 93 proteins in wild type strains, 40 of which were found to be dependent on IRE1. Our study reveals a cross-talk between ER- and mitochondrial proteostasis exemplified by an Ire1-dependent induction of Hsp60p, a mitochondrial chaperone. Thus, in this study we show changes in protein levels in various organelles in response to ER stress. A large fraction of these changes were dependent on canonical UPR signalling through Ire1, highlighting the importance of inter- organellar cross talk during stress..This article is protected by copyright. All rights reserved
    Proteomics 05/2014;
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    ABSTRACT: Differential expression of soluble proteins was explored in roots of metallicolous (M) and non-metallicolous (NM) plants of Agrostis capillaris L. exposed to increasing Cu to partially identify molecular mechanisms underlying higher Cu tolerance in M plants.Plants were cultivated 2 months on perlite with a CuSO4 (1–30 μM) spiked-nutrient solution. Soluble proteins extracted by the TCA/acetone procedure were separated with 2-DE (linear 4–7 pH gradient). After CCB staining and image analysis, 19 proteins differentially expressed were identified using LC-MS/MS and ESTs databases.At supra-optimal Cu exposure (15–30 μM), glycolysis was likely altered in NM roots with increased production of glycerone-P and methylglyoxal based on over-expression of Triosephosphate Isomerase and Fructose bisphosphate aldolase. Changes in Tubulins and higher expressions of 5-methyltetrahydropteroyltriglutamatehomocysteine methyltransferase and S-Adenosylmethionine synthase respectively underpinned impacts on the cytoskeleton and stimulation of ethylene metabolism. Increased L-methionine and S-Adenosylmethionine amounts may also facilitate production of nicotianamine, which complexes Cu, and L-cysteine, needed for metallothioneins and GSH. In M roots, the increase of [Cu/Zn] Superoxide dismutase suggested a better detoxification of superoxide, when Cu exposure rose. Higher Cu-tolerance of metallicolous plants would rather results from simultaneous cooperation of various processes than from a specific mechanism.This article is protected by copyright. All rights reserved
    Proteomics 05/2014;
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    ABSTRACT: Toxoplasma gondii is an obligatory intracellular apicomplexan parasite which exploits host cell surface components in cell invasion and intracellular parasitization. Sulfated glycans such as heparin and heparan sulfate have been reported to inhibit cell invasion by T. gondii and other apicimplexan parasites such as Plasmodium falciparum. The aim of this study was to investigate the heparin-binding proteome of T. gondii. The parasite-derived components were affinity-purified on the heparin moiety followed by mass-spectrometry finger-printing of the proteins. The heparin-binding proteins of T. gondii and P. falciparum were compared based on functionality and affinity to heparin. Among the proteins identified, the invasion-related parasite ligands derived from tachyzoite/merozoite surface and the secretory organelles were prominent. However, the profiles of the proteins were different in term of affinity to heparin. In T. gondii, the proteins with highest affinity to heparin were the intracellular components with functions of parasite development contrasted to that of P. falciparum, of which the rhoptry-derived proteins were prominently identified. The profiling of the heparin-binding proteins of the two apicomplexan parasites not only explained the mechanism of heparin-mediated host cell invasion inhibition, but also, to certain extents, revealed that the action of heparin on the parasite extended after endocytosis.This article is protected by copyright. All rights reserved
    Proteomics 05/2014;
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    ABSTRACT: Serum protein glycosylation is known to be affected by pathological conditions, including cancer and inflammatory diseases. Pancreatic cancer patients would benefit from early diagnosis, as the disease is often detected in an advanced stage and has poor prognosis. Searching for changes in serum protein site-specific glycosylation could reveal novel glycoprotein biomarkers. We used Sambucus nigra lectin affinity chromatography to enrich α-2,6 sialylated tryptic N-glycopeptides from albumin-depleted sera of pancreatic cancer patients, acute pancreatitis patients and healthy individuals, and compared their relative abundance using ultra performance liquid chromatography-mass spectrometry (LC-MS). Relative quantitation was done using the spectrum processing software MZmine. Identification was performed on the web-based tool GlycopeptideID, developed for in silico analysis of intact N-glycopeptides. Seventeen high-abundance serum proteins, mainly acute-phase proteins and immunoglobulins, with in total 27 N-glycosylation sites and 62 glycoforms, were identified. Pancreatitis patient sera contained 38 and pancreatic cancer patients sera 13 glycoform changes with statistical significance (P<0.05). In pancreatitis, up to 10-fold changes were found in some glycoforms, and in pancreatic cancer, 3-fold. Analysis showed that the changes often concerned one or two, but not all, N-glycosylation sites in a specific glycoprotein. In conclusion, the analysis shows that pancreatic cancer and acute pancreatitis are associated with changes in concentrations of intact sialylated N-glycopeptides derived from acute-phase proteins and immunoglobulins, and that the changes are site-specific.This article is protected by copyright. All rights reserved
    Proteomics 05/2014;

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