Journal of proteomics Impact Factor & Information

Publisher: Elsevier

Journal description

Current impact factor: 3.93

Impact Factor Rankings

2015 Impact Factor Available summer 2015
2013 / 2014 Impact Factor 3.929
2012 Impact Factor 4.088
2011 Impact Factor 4.878
2010 Impact Factor 5.074

Impact factor over time

Impact factor
Year

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5-year impact 0.00
Cited half-life 0.00
Immediacy index 0.00
Eigenfactor 0.00
Article influence 0.00
ISSN 1876-7737

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Elsevier

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Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Pneumococcal surface proteins are potential candidates for the development of protein-based vaccines and serological assays. The objective of the study was to develop a multiple bead-based immunoassay using Luminex xMAP® technology for the quantitation of natural antibodies against Streptococcus pneumoniae proteins and the characterization of the acute serum response following pneumococcal pneumonia in children. Sixty-four recombinantly produced pneumococcal proteins, which were selected based on their proteomic experimental identification by "shaving" live cells with trypsin followed by LC/MS/MS analysis, were coupled to fluorescent SeroMAP® beads and anti-pneumococcal specific IgG levels were determined in sera. Multiplex assay was validated through comparison of IgG levels to 14 randomly chosen pneumococcal antigens by using multiplex and singleplex assays. Acute serum IgG levels against RrgB were significantly lower in children ≤4years old with pneumococcal pneumonia than those in controls. In addition, there was a small trend toward slightly lower antibody levels for PrsA, RrgC and RrgB in pneumonia patients of the all age group. Copyright © 2015 Elsevier B.V. All rights reserved.
    Journal of proteomics 08/2015; 126. DOI:10.1016/j.jprot.2015.06.011
  • Apoorva Singh, Elavarasan Subramani, Chaitali DattaRay, Srikanth Rapole, Koel Chaudhury
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    ABSTRACT: Gestational diabetes mellitus (GDM) is the development of glucose intolerance in women after 20weeks of gestation and it affects 18% of pregnant women worldwide. GDM is considered a high-risk state which may lead to type II diabetes which is associated with an increase in a number of interrelated adverse perinatal outcomes. Given the fact that the progress of a successful pregnancy is dependent on the intricate communication between several biological molecules, identification of the proteomic profile perturbations in women with GDM is expected to help in understanding the disease pathogenesis and also discovery of clinical biomarker(s). In recent years, both gel-free and gel-based proteomics have been extensively investigated for improving maternal and child health. Although there are several reports integrating various aspects of proteomics in pregnancy related diseases such as preeclampsia, extensive Pubmed search shows no review so far on the application of proteomics in gestational diabetes. In this review, we focus on various high-throughput proteomic technologies for the identification of unique biosignatures and biomarkers responsible for the early prediction of GDM. Further, different analytical strategies and biological samples involved in proteomic analysis of this pregnancy-related disease are discussed. GDM refers to glucose intolerance which develops in women after 20weeks of gestation. The lack of uniformity in screening standards has led to rise in percentage of undetected cases in GDM. Thus, owing to the limitations of the current early pregnancy screening tools to identify women at risk of developing GDM, it is crucial to discover new biomarkers which can aid in disease identification and subsequent development. Proteomics relies on analysis of complete set of proteome for comprehensive understanding of complex biological processes and helps to gain insights into the molecular mechanisms of disease initiation and progression through monitoring cell activity in real time. Therefore, accurate early prediction of those destined to develop GDM would allow for early initiation of measures that may ameliorate the effects of this condition. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.07.020
  • Sylvie Luche, Elise Eymard-Vernain, Hélène Diemer, Alain Van Dorsselaer, Thierry Rabilloud, Cécile Lelong
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    ABSTRACT: Microorganisms, such as bacteria, are one of the first targets of nanoparticles in the environment. In this study, we tested the effect of two nanoparticles, ZnO and TiO2, with the salt ZnSO4 as the control, on the Gram-positive bacterium Bacillus subtilis by 2D gel electrophoresis-based proteomics. Despite a significant effect on viability (LD50), TiO2 NPs had no detectable effect on the proteomic pattern, while ZnO NPs and ZnSO4 significantly modified Bacillus subtilis metabolism. These results allowed us to conclude that the effects of ZnO observed in this work were mainly attributable to Zn dissolution in the culture media. Proteomic analysis highlighted twelve modulated proteins related to central metabolism: MetE and MccB (cysteine metabolism), OdhA, AspB, IolD, AnsB, PdhB and YtsJ (Krebs cycle) and XylA, YqjI, Drm and Tal (pentose phosphate pathway). Biochemical assays, such as free sulfhydryl, CoA-SH and malate dehydrogenase assays corroborated the observed central metabolism reorientation and showed that Zn stress induced oxidative stress, probably as a consequence of thiol chelation stress by Zn ions. The other patterns affected by ZnO and ZnSO4 were the stringent response and the general stress response. Nine proteins involved in or controlled by the stringent response showed a modified expression profile in the presence of ZnO NPs or ZnSO4: YwaC, SigH, YtxH, YtzB, TufA, RplJ, RpsB, PdhB and Mbl. An increase in the ppGpp concentration confirmed the involvement of the stringent response during a Zn stress. All these metabolic reorientations in response to Zn stress were probably the result of complex regulatory mechanisms including at least the stringent response via YwaC. This work, using a global analysis approach (2D gel electrophoresis), shows the physiological impact of two nanoparticles, TiO2 and ZnO, on the Gram-positive bacterium Bacillus subtilis. It deciphers the consequences of stress induced by ZnO nanoparticles or a zinc salt: central metabolism and sulfur amino acid metabolism reorientation as a result of thiol deprivation stress/oxidative stress, and the induction of the stringent response via YwaC synthase. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.07.018
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    ABSTRACT: The microbiological safety of milk is typically guaranteed by thermal treatments, such as pasteurization and ultra high temperature (UHT) treatment, whereas infant formula (IF) is often produced at even harsher conditions including a drying process. Thermal treatments have raised concerns, as they may denature proteins and initiate protein modifications. Previous studies identified already many lactosylation sites in milk and showed that the lactosylation degree of some proteins correlates to thermal treatment conditions. Here, we studied the glycation degrees of 124 lactosylation sites in 28 bovine milk proteins in raw milk, three brands of pasteurized milk, three brands of UHT milk, and five brands of IF. Whereas, the glycation degree of many lactosylation sites increased from raw milk, to pasteurized milk, UHT milk, and IF, several modification sites showed a different behavior indicating that global measures do not correctly reflect the reactivity of distinct sites. Interestingly, the glycation degrees varied much among the brands of UHT milk and IF indicating that specific production processes of a company have to be considered and not only the classification of milk as pasteurized or UHT. Thus, proper adjustments of the technical processes should allow reducing the lactosylation levels in both UHT milk and IF. It is well established that thermal treatment of milk triggers protein modifications, such as lactosylation of lysine residues in several proteins, although the extent of lactosylation has not been quantitatively compared for a broad panel of protein lactosylation sites among different commercial products. The current study extends previous reports by relatively quantifying 124 confirmed lactosylation sites in 28 bovine milk proteins including several low abundant proteins. Whereas, glycation is generally assumed to be an unspecific chemical reaction with the modification degrees depending on the protein and sugar concentrations, we could show that each protein and even each lactosylation site in a given protein is differently affected by thermal processes indicating that the global lactosylation degrees will not allow predicting the influence of a technical process on individual proteins and lactosylation sites. Additionally, we could show that brands of each milk product differ significantly in their glycation degrees with UHT milk brands for example spanning the whole range from the relatively low lactosylation degree of pasteurized milk to the rather high lactosylation degree of IF. Similar differences were obtained for IF that generally showed the highest glycation degree. The targeted quantification approach established and validated here will be useful to reveal technical processing steps that trigger individual lactosylation sites and thus can help to prevent such unwanted reactions. Even slight changes of the technical processes might allow reducing the lactosylation degree of milk proteins significantly without challenging the microbiological safety or affecting consumer behavior. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.07.021
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    ABSTRACT: This paper focuses on the gel-based membrane proteomics from diazotrophic cyanobacterium Anabaena PCC7120 by modifying the protocol of Hall et al. [1]. The bioinformatic analysis revealed that 59 (29 integral, 30 peripheral) of the 67 proteins identified were membrane proteins. Of the 29 integral proteins, except Alr0834, the remaining 28 contained 1-12 transmembrane helices. Sixteen integral proteins harboring signal peptides (Sec/TAT/LipoP) suggest that protein targeting in Anabaena involves both sec-dependent and sec-independent pathways. While majority of photosynthesis and respiration proteins (21 of 24) were confined to broad pH gradient the hypothetical and unknown (12 of 13), and cell envelope proteins (3 of 3) preferred the narrow pH range. Of the 5 transporters and binding proteins, Na(+)/H(+)- exchanging protein and Alr2372 were present in broad, pstS1 and cmpD in narrow and cmpA was common to both pH ranges. The distribution of proteins across pH gradient, thus clearly indicates the functional and structural diversity in membrane proteome of Anabaena. It requires mention that protochlorophyllide oxido-reductase, Na(+)/H(+)-exchanging protein, All1355, Alr2055, Alr3514, Alr2903 and Alr2751 were new entries to the 2DE membrane protein profile of Anabaena. This study demonstrates suitability of the modified protocol for the study of membrane protein from filamentous cyanobacteria. Anabaena sp. PCC7120 is used as model organism due to its agriculture significance as biofertilizer, close resemblance with higher plant chloroplast and availability of full genome sequence. Although cytosolic proteome has been explored a lot membrane proteins are still understudied as they are notoriously difficult to display using 2-D technology. Identification and characterization of these proteins is therefore required to elucidate and understand cellular mechanisms. The purpose of this study was to develop a protocol suitable for membrane protein extraction from Anabaena. Additionally, by homology comparison or domain assignment a possible function could be ascribed to novel uncharacterized proteins which will serve as a useful reference for further detailed studies of membrane system in filamentous cyanobacteria. Resolution of membrane proteins ranging from least (single transmembrane helix) to highly hydrophobic (several transmembrane helices) one on 2D gels recommends the gel based approach for identification of membrane proteomics from filamentous cyanobacteria. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.07.022
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    ABSTRACT: The reprogrammed lipopolysaccharide (LPS) pathway has been reported to render patients more susceptible to the development of post-traumatic multiple organ dysfunction syndrome (MODS). To facilitate thoroughly understanding this mechanism, a phosphoproteomic study was utilized to screen the potential signaling molecules. Interestingly, a truncated form of Src homology 2-domain-containing tyrosine phosphatase 1 (shp-1) emerged in human THP-1 macrophages sequentially treated with H2O2 and LPS and not with either of the treatments alone. Subsequent immunoblot analysis confirmed the cleavage of shp-1 and reduction of shp-1 activity in rat alveolar macrophages, mast cells, and neutrophils. Mechanistically, calpain is essential but not sufficient for shp-1 cleavage. In addition, shp-1 cleavage renders activation of phosphatidylinositol 3-kinase (PI-3K)/nuclear factor-κB (NF-κB) and mechanistic target of rapamycin complex 1 (mTORC1) in macrophages, resulting in enhanced cytokine induced neutrophil chemoattractant (CINC) secretion, which is critical for neutrophils recruitment in MODS. On the other hand, shp-1 cleavage results in activation of PI-3K/Akt, enhancing survival of neutrophils. Collectively, these results highlight the cleavage of shp-1 as a critical event in reprograming LPS pathway to promote both neutrophils recruitment and survival and provide a novel mechanistic framework for the investigation of the post-traumatic MODS. The LPS pathway reprogrammed by previous oxidative stress represents a mechanistic framework for studying post-resuscitation organ injury. However, the mechanism remains poorly elucidated. In the current study, utilizing a phosphoproteomic approach, we have revealed the cleavage of shp-1 following sequential H2O2 and LPS treatment in multiple types of hematopoietic cells. This cleavage may then lead to neutrophil recruitment through a dramatic increase in CINC secretion of macrophages, via PI-3K/NF-κB and mTORC1 activation. At the same time, this cleavage also renders neutrophils themselves more resistant to apoptosis via PI-3K/Akt. These findings hence provide a new rationale for cooperated signaling in different types of hematopoietic cells, which present a previously unknown mechanism that underlies the reprogramming of LPS pathway in response to previous oxidative stress. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.07.003
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    ABSTRACT: Cellular senescence causes profound changes in gene expression profile. In this study, we used a combined 2D-DIGE and nanoLC-ESI-LIT-MS/MS approach to evaluate the proteomic changes occurring both in replicative and stress-induced senescence of human IMR90 cells. Twenty protein spots were identified as shifting their quantitative representation in the same direction (over- or down-represented) in both conditions of senescence, which were associated with 25 sequence entries. Dedicated experiments demonstrated that the decreased representation of a set of these proteins is associated with the down-regulation of the corresponding mRNAs, indicating that the regulation of these genes during the senescence process occurs at a transcriptional level. We also performed functional studies by silencing nine of these genes in young cells, which demonstrated that RNA interference-mediated knockdown of LEPRE1, LIMA1/EPLIN, MAGOHA and MAGOHB induces a premature senescent phenotype in IMR90 cells. Chromatin immunoprecipitation experiments indicated that the reduced expression of these four genes is associated with changes in the histone methylation pattern of their promoters, as proved by the occurrence of increased repressive H3K27me3 along with decreased active H3K4me3 marks, respectively. Cellular senescence, a stable form of cell cycle arrest, is recognized as a phenomenon related to aging and age-related pathologies as well as interfering with tumor progression. Gene expression changes are closely associated with the onset of senescence but the molecular pathways regulating this process are still poorly understood. By using proteomics coupled to functional studies, we here show that both replicative and stress-induced senescence share quantitative modification of four novel proteins, in addition to others already reported in the literature. When ectopically down-regulated, corresponding four genes induce a premature senescence in young cells. The observed parallelism concerning the down-regulation of these genes both in vitro and in vivo senescent cells may foresee a possible biomarker role of the corresponding proteins in monitoring the progression of both aging and age-related diseases. In conclusion, these results for the first time highlight a possible role of LEPRE1, LIMA1/EPLIN, MAGOHA and MAGOHB in the biology of cellular senescence/aging, thus contributing to gain a deeper knowledge of the molecular mechanisms involved in the senescence program. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.07.010
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    ABSTRACT: We previously reported that knockout mice for α1,6-fucosyltransferase (Fut8), which catalyzes the biosynthesis of core-fucose in N-glycans, develop emphysema and that Fut8 heterozygous knockout mice are more sensitive to cigarette smoke-induced emphysema than wild-type mice. Moreover, a lower FUT8 activity was found to be associated with a faster decline in lung function among chronic obstructive pulmonary disease (COPD) patients. These results led us to hypothesize that core-fucosylation levels in a glycoprotein could be used as a biomarker for COPD. We focused on a lung-specific glycoprotein, surfactant protein D (SP-D), which plays a role in immune responses and is present in the distal airways, alveoli, and blood circulation. The results of a glycomic analysis reported herein demonstrate the presence of a core-fucose in an N-glycan on enriched SP-D from pooled human sera. We developed an antibody-lectin enzyme immunoassay (EIA) for assessing fucosylation (core-fucose and α1,3/4 fucose) in COPD patients. The results indicate that fucosylation levels in serum SP-D are significantly higher in COPD patients than in non-COPD smokers. The severity of emphysema was positively associated with fucosylation levels in serum SP-D in smokers. Our findings suggest that increased fucosylation levels in serum SP-D are associated with the development of COPD. It has been proposed that serum SP-D concentrations are predictive of COPD pathogenesis, but distinguishing between COPD patients and healthy individuals to establish a clear cut-off value is difficult because smoking status highly affects circulating SP-D levels. Herein, we focused on N-glycosylation in SP-D and examined whether or not N-glycosylation patterns in SP-D are associated with the pathogenesis of COPD. We performed an N-glycomic analysis of human serum SP-D and the results show that a core-fucose is present in its N-glycan. We also found that the N-glycosylation in serum SP-D was indeed altered in COPD, that is, fucosylation levels including core-fucosylation are significantly increased in COPD patients compared with non-COPD smokers. The severity of emphysema was positively associated with fucosylation levels in serum SP-D in smokers. Our findings shed new light on the discovery and/or development of a useful biomarker based on glycosylation changes for diagnosing COPD. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.07.011
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    ABSTRACT: Macrophages display large functional and phenotypical plasticity. They can adopt a broad range of activation states depending on their microenvironment. Various surface markers are used to characterize these differentially polarized macrophages. However, this is not informative for the functions of the macrophage. In order to have a better understanding of the functional changes of macrophages upon differential polarization, we studied differences in LPS- and IL4-stimulated macrophages. The THP-1 human monocytic cell line, was used as a model system. Cells were labeled, differentiated and stimulated with either LPS or IL-4 in a quantitative SILAC proteomics set-up. The resulting sets of proteins were functionally clustered. LPS-stimulated macrophages show increased secretion of proinflammatory peptides, leading to increased pressure on protein biosynthesis and processing. IL4-stimulated macrophages show upregulation of cell adhesion and extracellular matrix remodeling. Our approach provides an integrated view of polarization-induced functional changes and proves useful for studying functional differences between subsets of macrophages. Moreover, the identified polarization specific proteins may contribute to a better characterization of different activation states in situ and their role in various inflammatory processes. Macrophage activation states are often classified by a few surface or cytoplasmic markers. Although these markers are useful for a quick discrimination by techniques as flow cytometry, it provides no detailed information about functional differences. The significance of this paper is that we provide a model to study functional changes between differentially activated macrophages based on changes in protein abundancy. Evaluation of functional differences of macrophages in different (patho)physiological conditions may lead to a better understanding of the etiology of pathologies involving macrophages, such as cardiovascular diseases. Additionally, it may provide new markers or profiles to characterize macrophages. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.07.013
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    ABSTRACT: Shotgun proteomics generates valuable information from large-scale and target protein characterizations, including protein expression, protein quantification, protein post-translational modifications (PTMs), protein localization, and protein-protein interactions. Typically, peptides derived from proteolytic digestion, rather than intact proteins, are analyzed by mass spectrometers because peptides are more readily separated, ionized and fragmented. The amino acid sequences of peptides can be interpreted by matching the observed tandem mass spectra to theoretical spectra derived from a protein sequence database. Identified peptides serve as surrogates for their proteins and are often used to establish what proteins were present in the original mixture and to quantify protein abundance. Two major issues exist for assigning peptides to their originating protein. The first issue is maintaining a desired false discovery rate (FDR) when comparing or combining multiple large datasets generated by shotgun analysis and the second issue is properly assigning peptides to proteins when homologous proteins are present in the database. Herein we demonstrate a new computational tool, ProteinInferencer, which can be used for protein inference with both small- or large-scale data sets to produce a well-controlled protein FDR. In addition, ProteinInferencer introduces confidence scoring for individual proteins, which makes protein identifications evaluable. The manuscript describes an approach to assess the analysis of large-scale proteomic projects by creating a consistent protein FDR across all experiments. A confidence score is calculated for each of identified proteins. ProteinInferencer provides a proper way to compare protein and peptides identification among large number of mass spectrometry experiments. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.07.006
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    ABSTRACT: Recent progress in snake venomics has shed much light on the intra-species variation among the toxins from different geographical regions and has provided important information for better snakebite management. Most previous reports on snake venomics were based on venoms pooled from different snakes. In this study, we present the proteomic and glycomic profiles of venoms from individual Naja atra snakes. The results reveal wide dynamic range of three-finger toxins. Systematic classification based on cardiotoxin (CTX-) profiles of A2/A4 and A6, respectively, allowed the identification of two putative subspecies of Taiwan cobra from the eastern and western regions. We also identified four major N-glycan moieties on cobra snake venom metalloproteinase on the bi-antennary glycan core. ELISA showed that these glycoproteins (<3%) could elicit much higher antibody response in antiserum when compared to other high-abundance cobra venom toxins such as small molecular weight CTXs (~60%). By removing these high-molecular weight glycoproteins from the immunogen, we demonstrated better protection than that achieved with conventional crude venom immunization in mice challenged by crude venom. We conclude that both intra-species and inter-individual variation of proteomic and glycomic profiles of snake venomics should be considered to provide better antivenomic approach for snakebite management. Based on the proteomic and glycomic profiles of venoms obtained from individual snakes, we demonstrated a surprisingly wide dynamic range and geographical variation of three-finger toxins in cobra venomics. This provides a reasonable explanation for the variable neutralization effects of antivenom treatment on victims suffering from cobra snakebite and suggests a simple and economic method to produce potent antivenom with better efficacy. Since two major venomic profiles with distinct dynamic ranges were observed for Taiwan cobra venoms isolated from the eastern and western regions, the current venomic profile should be used as a quality control for future production of antivenom in clinical applications. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.07.015
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    ABSTRACT: Label-free LC-MS/MS proteomics has proven itself to be a powerful method for evaluating protein identification and quantification from complex samples. For comparative proteomics, several methods have been used to detect the differential expression of proteins from such data. We have assessed seven methods used across the literature for detecting differential expression from spectral count quantification: Student's t-test, significance analysis of microarrays (SAM), normalised spectral abundance factor (NSAF), normalised spectral abundance factor-power law global error model (NSAF-PLGEM), spectral index (SpI), DESeq and QSpec. We used 2,000 simulated datasets as well as publicly available data from a proteomics standards study to assess the ability of these methods to detect differential expression in varying effect sizes and proportions of differentially expressed proteins. At two false discovery rate (FDR) levels, we find that several of the methods detect differential expression within the data with reasonable precision, others detect differential expression at the expense of low precision, and finally, others which fail to identify any differentially expressed proteins. The inability of these seven methods to fully capture the differential landscape, even at the largest effect size, illustrates some of the limitations of the existing technologies and the statistical methodologies. In label-free mass spectrometry experiments, protein identification and quantification have always been important, but there is now a growing focus on comparative proteomics. Detecting differential expression in protein levels can inform on important biological mechanisms and provide direction for further study. Given the high cost and labour intensive nature of validation experiments, statistical methods are important for prioritizing proteins of interest. Here, we have performed a comparative analysis to investigate the statistical methodologies for detecting differential expression and provide a reference for future experimental designs. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.07.012
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    ABSTRACT: The goat whey proteome has been explored in depth via capture with combinatorial peptide ligand libraries (CPLL) at three different pH values. A total of 452 unique species has been tabulated, a proteome discovery so far unmatched in any single other investigation of milk from any mammalian species. This massive discovery is probably related to: i) the extraordinary load of proteins onto the CPLL beads (i.e. two grams for each different pH capture) vs. barely 100μL of beads; ii) the high resolution/high mass accuracy of mass spectral data; and iii) the use of two complementary tools, Mascot and PEAKS, each one contributing to a set of unique protein IDs. Due to the relative paucity of available protein annotations for goat, only 10% of the identified proteins belong to the capra, whereas 52% are specific of sheep and 37% are homologous to that of bovine milk. This work reports the largest description so far of the goat milk proteome, which has been compared with cow's milk proteome and would thus help to understand the importance of low-abundance proteins with respect to the unique biological properties of this nutrient. Many investigations have reported real benefits from using non-bovine milks as an alternative in cases of cow's milk allergy. However, allergies to non-bovine milk proteins have also been documented. In this contest, the use of goat's milk for feeding healthy babies or as a possible alternative to cow's milk for allergic subjects is still debated. In recent years, different studies have reported a comparison of the milk proteome profiles of some animal species, including goat, for identifying sources of hypoallergenic alternatives to bovine milk, but they deal only with the characterization of the most abundant species. Indeed, up to this day, the exploration of the less abundant proteins has only just recently been reported for bovine, swine and donkey, whereas not much is known about the repertoire of low-abundance proteins in goat milk. This work reports the largest description of the goat milk proteome (452 unique gene products). This huge discovery has been related to the use of the well-ingrained CPLL sample pre-treatment, the unique scan rate, very high resolution and accuracy of the mass spectrometer here employed and, finally, to the use of two complementary database search tools. This list of identified proteins could serve as a starting point for a comparison with cow's milk proteome and would help to understand the importance of low-abundance proteins with respect to the unique biological properties of goat milk. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.07.009
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    ABSTRACT: Nemopilema nomurai is one of the largest species of jellyfish in the world. It blooms mainly offshore of Korea, China, and Japan. Increasing population numbers of N. nomurai is increasing the risk of sea bathers to the jellyfish stings and accompanying envenomations. Cardiovascular effects, and cytotoxicity and hemolytic activities have been previously reported in rodent models. To understand the mechanism of cardiac toxicity, we examined the effect of N. nomurai jellyfish venom (NnV) at the proteome level on rat cardiomyocytes cell line H9c2 using two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS). Cells treated with NnV displayed dose-dependent inhibition of viability. Cellular changes at proteome level were investigated after 6h and 12h of venom treatment. Electrophoretic examination revealed 72 protein spots displaying significant quantitative changes. These proteins were analyzed by MALDI-TOF/MS. Thirty four differentially expressed proteins were successfully identified; 24 proteins increased in quantity and 10 proteins decreased, compared to the respective controls. Proteins altered in content in Western blot analyses included myosin VII, annexin A2, aldose reductase, suppressor of cytokine signaling 1 (SOCS1), and calumenin, which are well-known marker proteins of cardiac dysfunctions. This is the first report revealing the cardiac toxicity of NnV at the proteome level. NnV directly targeted proteins involved in cardiac dysfunction or maintenance. Suppressor of cytokine signaling 1 (SOCS1), which inhibits the Janus kinase/signal transducers and activators of transcription (JAK/STAT) pathway, was upregulated by NnV. Other proteins related to cardiac arrest that were over-expressed included aldose reductase and calumenin. These results clarify the underlying mechanism of cardiomyocyte damage caused by NnV. By inhibiting these particular targets and more precisely identifying the components of NnV-mediated cardiac toxicity, jellyfish venom-associated poisoning could be reduced or prevented. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.07.008
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    ABSTRACT: The black yeast Exophiala dermatitidis is a worldwide distributed agent of primary and secondary diseases in both immunocompromised and healthy humans, with a high prevalence in human-made environments. Since thermo-tolerance has a crucial role in the fungus persistence in man-dominated habitat and in its pathogenicity, three incubation temperatures (37, 45, 1°C) and two timespans (1hour, 1week) were selected to simulate different environmental conditions and to investigate the effect of temperature on the proteome of E. dermatitidis CBS 525.76. Using a novel protocol for protein extraction from black yeasts, 2-D DIGE could be applied for characterization of changes in total protein spot abundance among the experimental conditions. A total of 32 variable proteins were identified by mass spectrometry. Data about protein functions, localization and pathways were also obtained. A typical stress response under non-optimal temperature could not be observed at the proteome level, whereas a reduction of the metabolic activity, mostly concerning processes as the general carbon metabolism, was detected after exposure to cold. These results suggest that a fine protein modulation takes place following temperature treatment and a repertoire of stable protein might be at the base of E. dermatitidis adaptation to altered growth conditions. E. dermatitidis is a pathogenic black yeast causing neurotropic infections, systemic and subcutaneous disease in a wide range of hosts, including humans. The discovery of the fungus high prevalence in man-made habitats, including sauna facilities, drinking water and dishwashers, generated concern and raised questions about the infection route. In the present work - which is the first contribution on E. dermatitidis proteome - the effect of different temperature conditions on the fungus protein pattern have been analysed by using a gel-based approach and the temperature responsive proteins have been identified. The absence of a typical stress response following the exposure to non-optimal temperature was detected at the proteome level, along with a general reduction of the metabolic activity after exposure to cold. These results suggest that a very fine regulation of the protein expression as well as adaptations involving a basic set of stable proteins may be at the base of E. dermatitidis enormous ecological plasticity, which plays a role in the fungus distribution, also enabling the transition from natural to human habitat and to the human host. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.07.007
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    ABSTRACT: With the growing amount of experimental data produced in proteomics experiments and the requirements / recommendations of journals in the proteomics field to publicly make available data described in papers, a need for long-term storage of proteomics data in public repositories arises. For such an upload one needs proteomics data in a standardized format. Therefore, it is desirable, that the proprietary vendor's software will integrate in the future such an export functionality using the standard formats for proteomics results defined by the HUPO-PSI group. Currently not all search engines and analysis tools support these standard formats. In the meantime there is a need to provide user-friendly free-to-use conversion tools that can convert the data into such standard formats in order to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories. ProCon is such a conversion tool written in Java for conversion of proteomics identification data into standard formats mzIdentML and Pride XML. It allows the conversion of Sequest(TM) / Comet .out files, of search results from the popular and often used ProteomeDiscoverer® 1.x (x=versions 1.1 to1.4) software and search results stored in the LIMS systems ProteinScape® 1.3 and 2.1 into mzIdentML and PRIDE XML. Biological Significance This paper describes the ProCon converter, which allows to convert peptide and protein identification results from Sequest.out, ProteinScape® and ProteomeDiscoverer® result files into the standard format mzIdentML, which is recommended for the upload into the major proteomics data repositories via ProteomeXchange. Compared with M2Lite it creates mzIdentML files enriched with additional information like e.g. pI values, sample names and more complete annotations by extensive usage of CV terms. It also allows the inclusion of the protein identifications into the ProteinDetectionList of mzIdentML, which is important because for the biological interpretation the proteins and not the peptides are of interest. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.06.015
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    ABSTRACT: Sea stars rely on epidermal secretions to cope with their benthic life. Their integument produces a mucus, which represents the first barrier against invaders; and their tube feet produce adhesive secretions to pry open mussels and attach strongly but temporarily to rocks. In this study, we combined high-throughput sequencing of expressed mRNA and mass-spectrometry-based identification of proteins to establish the first proteome of mucous and adhesive secretions from the sea star A. rubens. We show that the two secretions differ significantly, the major adhesive proteins being only present in trace amounts in the mucus secretion. Excepted for 41 proteins which were present in both secretions, a total of 34 and 244 proteins were identified as specific of adhesive secretions and mucus, respectively. We discuss the role of some of these proteins in the adhesion of sea stars as well as in their protection against oxygen reactive species and microorganisms. In addition, 58% of the proteins identified in adhesive secretions did not present significant similarity to other known proteins, revealing a list of potential novel sea star adhesive proteins uncharacterized so far. The panel of proteins identified in this study offers unprecedented opportunities for the development of sea star-inspired biomimetic materials. In this study, we combined high-throughput sequencing of mRNA (transcriptome analysis) and mass-spectrometry-based identification of proteins to establish the first proteome of mucous and adhesive secretions from the sea star Asterias rubens. We show that, although both secretions are produced by the epidermis, they differ significantly in terms of protein composition. We present for the first time a complete list of proteins potentially involved in sea star adhesion, most of which appear to correspond to novel proteins uncharacterized so far. In the mucus proteome, we identified a panel of proteins involved in the protection against oxygen reactive species and microorganisms. Overall, these results set the scene for future studies aimed at characterizing novel water resistant adhesive molecules as well as proteins with anti-microbial properties. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.07.002
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    ABSTRACT: ProLuCID, a new algorithm for peptide identification using tandem mass spectrometry and protein sequence databases has been developed. This algorithm uses a three tier scoring scheme. First, a binomial probability is used as a preliminary scoring scheme to select candidate peptides. The binomial probability scores generated by ProLuCID minimize molecular weight bias and are independent of database size. A modified cross-correlation score is calculated for each candidate peptide identified by the binomial probability. This cross-correlation scoring function models the isotopic distributions of fragment ions of candidate peptides which ultimately results in higher sensitivity and specificity than that obtained with the SEQUEST XCorr. Finally, ProLuCID uses the distribution of XCorr values for all of the selected candidate peptides to compute a Z score for the peptide hit with the highest XCorr. The ProLuCID Z score combines the discriminative power of XCorr and DeltaCN, the standard parameters for assessing the quality of the peptide identification using SEQUEST, and displays significant improvement in specificity over ProLuCID XCorr alone. ProLuCID is also able to take advantage of high resolution MS/MS spectra leading to further improvements in specificity when compared to low resolution tandem MS data. A comparison of filtered data searched with SEQUEST and ProLuCID using the same false discovery rate as estimated by a target-decoy database strategy, shows that ProLuCID was able to identify as many as 25% more proteins than SEQUEST. ProLuCID is implemented in Java and can be easily installed on a single computer or a computer cluster. The manuscript describes ProLuCID, a new algorithm for peptide identification using tandem mass spectrometry and protein sequence databases. This algorithm uses a three tier scoring scheme. First, a binomial probability is used as a preliminary scoring scheme to select candidate peptides. The binomial probability scores generated by ProLuCID minimize molecular weight bias and are independent of database size. A modified cross-correlation score is calculated for each candidate peptide identified by the binomial probability. This cross-correlation scoring function models the isotopic distributions of fragment ions of candidate peptides which ultimately results in higher sensitivity and specificity than that obtained with the SEQUEST XCorr. Finally, ProLuCID uses the distribution of XCorr values for all of the selected candidate peptides to compute a Z score for the peptide hit with the highest XCorr. The ProLuCID Z score combines the discriminative power of XCorr and DeltaCN, the standard parameters for assessing the quality of the peptide identification using SEQUEST, and displays significant improvement in specificity over ProLuCID XCorr alone. ProLuCID is also able to take advantage of high resolution MS/MS spectra leading to further improvements in specificity when compared to low resolution tandem MS data. A comparison of filtered data searched with SEQUEST and ProLuCID using the same false discovery rate as estimated by a target-decoy database strategy, shows that ProLuCID was able to identify as many as 25% more proteins than SEQUEST. Copyright © 2015. Published by Elsevier B.V.
    Journal of proteomics 07/2015; DOI:10.1016/j.jprot.2015.07.001