Journal of Proteome Research (J PROTEOME RES )

Publisher: American Chemical Society


The Journal of Proteome Research (JPR) provides content encompassing all aspects of systems-oriented, global protein analysis and function, emphasizing the synergy between physical and life sciences resulting in a multi-disciplinary approach to the understanding of biological processes. JPR integrates the fields of chemistry, mathematics, applied physics, biology, and medicine in order to better understand the function of proteins in biological systems. In addition to publishing original peer-reviewed research papers, JPR also publishes research highlights, current events, book and software reviews, and a calendar of upcoming short courses and symposia of interest to proteomic scientists.

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  • Website
    Journal of Proteome Research website
  • Other titles
    Journal of proteome research (Online), Journal of proteome research, Proteome research, JPR
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  • Material type
    Document, Periodical, Internet resource
  • Document type
    Internet Resource, Computer File, Journal / Magazine / Newspaper

Publisher details

American Chemical Society

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    • Author cannot archive a pre-print version
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    • Must obtain written permission from Editor
    • Must not violate ACS ethical Guidelines
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    • Author cannot archive a post-print version
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    • If mandated by funding agency or employer/ institution
    • Must obtain written permission from Editor confirming posting does not conflict prior publication policies
    • If mandated to deposit before 12 months, must obtain waiver from Institution/ Agency or use AuthorChoice
    • 12 months
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    • On website or repositories
    • Non-Commercial
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    • If mandated sooner than 12 months, must obtain waiver from Editors or use AuthorChoice
    • Publisher's version/PDF may be used, but only via AuthorChoice option
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Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Protein carbonylation is a common nonenzymatic oxidative post-translational modification, which is often considered as biomarker of oxidative stress. Recent evidence links protein carbonylation also to obesity and type 2 diabetes mellitus (T2DM), though the protein targets of carbonylation in human plasma have not been identified. In this study, we profiled carbonylated proteins in plasma samples obtained from lean individuals and obese patients with or without T2DM. The plasma samples were digested with trypsin, carbonyl groups were derivatized with O-(biotinylcarbazoylmethyl)hydroxylamine, enriched by avidin affinity chromatography, and analyzed by RPC-MS/MS. Signals of potentially modified peptides were targeted in a second LC-MS/MS analysis to retrieve the peptide sequence and the modified residues. A total of 158 unique carbonylated proteins were identified, of which 52 were detected in plasma samples of all three groups. Interestingly, 36 carbonylated proteins were detected only in obese patients with T2DM, whereas 18 were detected in both nondiabetic groups. The carbonylated proteins originated mostly from liver, plasma, platelet, and endothelium. Functionally, they were mainly involved in cell adhesion, signaling, angiogenesis, and cytoskeletal remodeling. Among the identified carbonylated proteins were several candidates, such as VEGFR-2, MMP-1, argin, MKK4, and compliment C5, already connected before to diabetes, obesity and metabolic diseases.
    Journal of Proteome Research 07/2014;
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    ABSTRACT: Stationary-phase, carbon-starved shake-flask cultures of Saccharomyces cerevisiae are popular models for studying eukaryotic chronological ageing. However, their nutrient-starved physiological status differs substantially from that of post-mitotic metazoan cells. Retentostat cultures offer an attractive alternative model system in which yeast cells, maintained under continuous calorie restriction, hardly divide but retain high metabolic activity and viability for prolonged periods of time. Using TMT labeling and UHPLC-MS/MS, the present study explores the proteome of yeast cultures during transition from exponential growth to near-zero growth in severely calorie-restricted retentostats. This transition elicited protein level changes in 20% of the yeast proteome. Increased abundance of heat-shock-related proteins correlated with increased transcript levels of the corresponding genes and was consistent with a strongly increased heat-shock tolerance of retentostat-grown cells. A sizeable fraction (43%) of the proteins with increased abundance under calorie restriction was involved in oxidative phosphorylation and in various mitochondrial functions that, under the anaerobic, non-growing conditions used, have a very limited role. While it may seem surprising that yeast cells confronted with severe calorie restriction invest in the synthesis of proteins that, under those conditions, do not contribute to fitness, these responses may confer metabolic flexibility and thereby a selective advantage in fluctuating natural habitats.
    Journal of Proteome Research 07/2014;
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    ABSTRACT: Ewing sarcoma is a cancer of bone and soft tissue in children that is characterized by a chromosomal translocation involving EWS and an Ets family transcription factor, most commonly Fli-1. EWS-Fli-1 fusion accounts for 85% of cases. The growth and survival of Ewing sarcoma cells are critically dependent on EWS-Fli-1. A large body of evidence has established that EWS-Fli-1 functions as a DNA-binding transcription factor that regulates the expression of a number of genes important for cell proliferation and transformation. However, little is known about the biochemical properties of the EWS-Fli-1 protein. We undertook a series of proteomic analyses to dissect the EWS-Fli-1 interactome. Employing a proximity-dependent biotinylation technique, BioID, we identified cation-independent mannose 6-phosphate receptor (CIMPR) as a protein located in the vicinity of EWS-Fli-1 within a cell. CIMPR is a cargo that mediates the delivery of lysosomal hydrolases from trans-Golgi network to endosome, which are subsequently transferred to the lysosomes. Further molecular cell biological analyses uncovered a role for lysosomes in the turnover of the EWS-Fli-1 protein. We demonstrate that an mTORC1 active-site inhibitor torin 1, which stimulates the TFEB-lysosome pathway, can induce the degradation of EWS-Fli-1, suggesting a potential therapeutic approach to target EWS-Fli-1 for degradation.
    Journal of Proteome Research 07/2014;
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    ABSTRACT: Epidermal homeostasis is a balancing act governed by a multitude of underlying regulatory events, and several growth factors and signaling pathways have been implicated in regulation of the balance between proliferation and differentiation in keratinocytes. We show here that the signal transducer/transcription factor FIZ1 (Flt3 interacting zinc finger protein-1) is a previously unknown player in this regulatory axis, promoting an increase in proliferation of HaCaT human immortalized keratinocytes that is driven by more rapid G1/S progression and mediated by activation of the MAP/ERK kinase pathway. Utilizing quantitative SILAC-based secretome analysis, we identified the insulin growth factor binding protein IGFBP3 as the key mediating factor, demonstrating that elevated FIZ1 levels promote increased IGFBP3 expression and secretion and a concurrent increased sensitivity to IGF1 signaling, while antibody-based neutralization of IGFBP3 abrogates the FIZ1-induced growth advantage. To identify underlying protein-protein interactions likely to govern these events, we mapped the interactome of FIZ1 and found eight novel binding partners that form complexes with the protein in the cytoplasm and nucleus. These include signal transduction and transcription factors and the cell cycle regulatory NDR (Nuclear Dbf2-related) kinases. Our results provide further insight into the complex balance of epidermal homeostasis and identify FIZ1 as a novel therapeutic target.
    Journal of Proteome Research 06/2014;
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    ABSTRACT: Myostatin, a highly conserved secretory protein negatively regulates muscle development affecting both proliferation and differentiation of muscle cells. Proteolytic processing of the myostatin precursor protein generates a myostatin pro-peptide and mature protein. Dimerization of the mature myostatin protein creates the active myostatin form. Myostatin dimer activity can be inhibited by non-covalent binding of two monomeric myostatin pro-peptides. This ability for myostatin to self-regulate and altered expression of myostatin in states of abnormal health (e.g. muscle wasting) support the need for specific detection of myostatin forms. Current protein detection methods (e.g. Western blot) rely greatly on antibodies and are semi-quantitative at best. Tandem mass spectometry (as in this study) provides a highly specific method of detection, enabling the characterisation of myostatin protein forms through the analysis of discrete peptides fragments. Utilizing the scheduled high-resolution multiple reaction monitoring paradigm (sMRMHR; AB SCIEX 5600 TripleTOF) we identified the lower limit of quantitation (LLOQ) of both mature (DFGLDCDEHSTESR) and pro-peptide regions (ELIDQYDVQR) as 0.19nmol/L. Furthermore, scheduled multiple reaction monitoring (sMRM; AB SCIEX QTRAP® 5500) identified a LLOQ for apeptide of the pro-peptide region (LETAPNISK) as 0.16nmol/L and a peptide of the mature region (EQIIYGK) as 0.25nmol/L.
    Journal of Proteome Research 06/2014;
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    ABSTRACT: Autoimmune hepatitis (AIH) is confoundable with other liver diseases due to shared nonspecific symptoms and serological and histological overlaps. This study compared the plasma metabolomic profiles of patients with AIH, primary biliary cirrhosis (PBC), PBC/AIH overlap syndrome (OS), and drug-induced liver injury (DILI) with those of healthy subjects to identify potential biomarkers of AIH. Metabolomic profiling and biomarker screening were performed using proton nuclear magnetic resonance spectroscopy (1H-NMR) coupled with a partial least squares discriminant analysis. Compared with the healthy volunteers and the other liver disease patients, the AIH patients exhibited relatively high levels of plasma pyruvate, lactate, acetate, acetoacetate, and glucose. Such metabolites are typically related to energy metabolism alterations and may be a sign of metabolic conversion to the aerobic glycolysis phenotype of excessive immune activation. Increased aromatic amino acids and decreased branched chain amino acids were found in the plasma from the AIH patients. The whole NMR profiles were stepwise reduced, and 9 metabolomic biomarkers with the greatest significance in the discriminant analysis were obtained. The diagnostic utility of the selected metabolites was assessed, and these biomarkers achieved good sensitivity, specificity, and accuracy (all above 93%) in distinguishing AIH from PBC, DILI, and OS. This report is the first to present the metabolic phenotype of AIH and the potential utility of 1H-NMR metabolomics in the diagnosis of AIH.
    Journal of Proteome Research 06/2014;
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    ABSTRACT: Members of the 2-aminobenzamide class of histone deacetylase (HDAC) inhibitors show promise as therapeutics for the neurodegenerative diseases Friedreich's ataxia (FRDA) and Huntington's disease (HD). While it is clear that HDAC3 is one of the important targets of the 2-aminobenzamide HDAC inhibitors, inhibition of other class I HDACs (HDACs 1 and 2) may also be involved in the beneficial effects of these compounds in FRDA and HD, and other HDAC interacting proteins may be impacted by the compound. To this end, we synthesized activity-based profiling probe (ABPP) versions of one of our HDAC inhibitors (compound 106), and in the present study we used a quantitative proteomic method coupled with multidimensional protein identification technology (MudPIT) to identify the proteins captured by the ABPP 106 probe. Nuclear proteins were extracted from FRDA patient iPSC-derived neural stem cells, and then were reacted with control and ABPP 106 probe. After reaction, the bound proteins were digested on the beads and the peptides were modified using stable isotope labeled formaldehyde to form dimethyl amine. The selectively bound proteins determined by mass spectrometry were subjected to functional and pathway analysis. Our findings suggest that the targets of compound 106 are not only involved in transcriptional regulation, but also in posttranscriptional processing of mRNA.
    Journal of Proteome Research 06/2014;
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    ABSTRACT: Neuropathic pain frequently occurs in a wide variety of diseases or post-surgeries as a result of injuries to the central and peripheral nervous system causing disorders of pain signaling. Unfortunately, the underlying biological mechanism of neuropathic pain is still not well understood. This paper is focused on studying the changes of protein expression in the dorsal spinal cord of rats with spinal nerve ligation (SNL). By comparing the protein expression in SNL group and control group, pain related proteins could be identified. In this study we used a labeling based proteomic method together with high resolution mass spectrometry for proteome analysis. In our results, 36 proteins were found to be significant differently expressed in SNL group. Combined with the bio-pathway analysis tool, these significant proteins are found as strongly involved in signaling process. Furthermore, synapsin 1 and microtubule-associated protein 2 were found to be the most prominent pain related proteins in this study, which provide us with a new hypothesis of the mechanism resulting in neuropathic pain.
    Journal of Proteome Research 06/2014;
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    ABSTRACT: Experimental autoimmune encephalomyelitis (EAE) is a murine model of multiple sclerosis, a chronic neurodegenerative and inflammatory autoimmune condition of the central nervous system (CNS). Pathology is driven by the infiltration of autoreactive CD4(+) lymphocytes into the CNS where they attack neuronal sheaths causing ascending paralysis. We used an isotope-coded protein labelling approach to investigate the proteome of CD4(+) cells isolated from the spinal cord and brain of mice at various stages of EAE progression in two EAE disease models; PLP139-151-induced relapsing-remitting EAE and MOG35-55-induced chronic EAE, which emulate the two forms of human multiple sclerosis. A total of 1120 proteins were quantified across disease onset, peak-disease and remission phases of disease and of these, 13 up-regulated proteins of interest were identified with functions relating to the regulation of inflammation, leukocyte adhesion and migration, tissue repair and the regulation of transcription/translation. Proteins implicated in processes such as inflammation (S100A4 and S100A9) and tissue repair (Annexin A1), which represent key events during EAE progression were validated by quantitative PCR. This is the first targeted analysis of autoreactive cells purified from the CNS during EAE, highlighting fundamental CD4(+) cell-driven processes that occur during the initiation of relapse and remission stages of disease. The data have been deposited to the ProteomeXchange with identifier PXD001011.
    Journal of Proteome Research 06/2014;
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    ABSTRACT: Glioblastoma multiforme (GBM) is the most aggressive malignant primary brain tumor with a dismal mean survival even with the current standard of care. Although in vitro cell systems can provide mechanistic insight into the regulatory networks governing GBM cell proliferation and migration, clinical samples provide a more physiologically relevant view of oncogenic signaling networks. However, clinical samples are not widely available and may be embedded for histopathologic analysis. With the goal of accurately identifying activated signaling networks in GBM tumor samples, we investigated the impact of embedding in optimal cutting temperature (OCT) compound followed by flash freezing in LN2 vs. immediate flash freezing (iFF) in LN2 on protein expression and phosphorylation-mediated signaling networks. Quantitative proteomic and phosphoproteomic analysis of 8 pairs of tumor specimens revealed minimal impact of the different sample processing strategies and highlighted the large inter-patient heterogeneity present in these tumors. Correlation analyses of the differentially processed tumor sections identified activated signaling networks present in selected tumors and revealed the differential expression of transcription, translation, and degradation associated proteins. This study demonstrates the capability of quantitative mass spectrometry for identification of in vivo oncogenic signaling networks from human tumor specimens that were either OCT-embedded or immediately flash-frozen.
    Journal of Proteome Research 06/2014;