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Journal of Proteome Research

Simon Davis, Connor Scott, Olaf Ansorge, Roman Fischer
While nearly comprehensive proteome coverage can be achieved from bulk tissue or cultured cells, the data usually lacks spatial resolution. As a result, tissue based proteomics averages protein abundance across multiple cell types and/or localisations. With proteomics platforms lacking sensitivity and throughput to undertake deep single-cell proteome studies in order to resolve spatial or cell type dependent protein expression gradients within tissue, proteome analysis has been combined with sorting techniques to enrich for certain cell populations...
February 15, 2019: Journal of Proteome Research
Sven-Bastiaan Haange, Nico Jehmlich, Maximilian Hoffmann, Klaus Weber, Jörg Lehmann, Martin von Bergen, Ulla Slanina
Using the acute dextran sulfate sodium (DSS)-induced colitis model, studies have demonstrated that intestinal inflammation is accompanied by major changes in the composition of the intestinal microbiota. Only little is known about the microbial changes and more importantly their functional impact in the chronic DSS colitis model. We used a refined model of chronic DSS-induced colitis that reflects typical symptoms of the human disease without detrimental weight loss usually observed in DSS models. We sampled cecum and colon content as well as colon mucus from healthy and diseased mouse cohorts (n=12) and applied 16S rRNA gene sequencing and metaproteomics...
February 15, 2019: Journal of Proteome Research
Paul D Veith, Michelle D Glew, Dhana G Gorasia, Dina Chen, Neil M O'Brien-Simpson, Eric C Reynolds
The identification and localisation of outer membrane proteins (Omps) and lipoproteins in pathogenic treponemes such as T. denticola (periodontitis) and T. pallidum (syphilis) has been challenging. In this study, label-free quantitative proteomics using MaxQuant was applied to naturally produced outer membrane vesicles (OMVs) and cellular fractions to identify 1448 T. denticola proteins. Of these, 90 proteins were localised to the outer membrane (OM) comprising 59 lipoproteins, 25 β-barrel proteins and six other putative OM-associated proteins...
February 14, 2019: Journal of Proteome Research
Dalia Elinger, Alexandra Gabashvili, Yishai Levin
Analysis of cells and tissue by bottom up proteomics starts with lysis, followed by in-solution digestion. Lysis buffers commonly used include detergents and other reagents for achieving efficient protein solubility. However these reagents are, for the most part, incompatible with downstream analytical instrumentation. One method for in-solution digestion and cleanup, termed Suspension Trapping (S-Trap), has been recently introduced. We present an evaluation of the compatibility of commonly used lysis buffers with S-trap: SDS, urea, NP-40, RIPA and SDS with DTT (SDT)...
February 14, 2019: Journal of Proteome Research
Chaevien S Clendinen, David A Gaul, Maria Eugenia Monge, Rebecca S Arnold, Arthur S Edison, John A Petros, Facundo M Fernandez
Technological advances in mass spectrometry (MS), liquid chromatography (LC) separations, nuclear magnetic resonance (NMR) spectroscopy, and big data analytics have made possible studying metabolism at an "omics" or systems level. Here, we applied a multi-platform (NMR+LC-MS) metabolomics approach to the study of preoperative metabolic alterations associated with prostate cancer recurrence. Thus far, predicting which patients will recur even after radical prostatectomy has not been possible. Correlation analysis on metabolite abundances detected on serum samples collected prior to surgery from prostate cancer patients (n=40 remission vs...
February 13, 2019: Journal of Proteome Research
Tharindu Fernando, Annick Sawala, Andrew Bailey, Alex P Gould, Paul C Driscoll
The measurement of absolute metabolite concentrations in small samples remains a significant analytical challenge. This is particularly the case when the sample volume is only a few microlitres or less and cannot be determined accurately via direct measurement. We previously developed volume determination with two standards (VDTS) as a method to address this challenge for biofluids. As a proof-of-principle, we applied VDTS to NMR spectra of polar metabolites in the hemolymph (blood) of the tiny yet powerful genetic model Drosophila melanogaster...
February 13, 2019: Journal of Proteome Research
Chih-Yung Chiu, Mei-Ling Cheng, Kin-Sun Wong, Shen-Hao Lai, Meng Han Chiang, Ming-Han Tsai, Gigin Lin
Fibrin formation in infectious parapneumonic effusion (IPE) characterizes complicated parapneumonic effusion and is important for providing guidelines for management of IPEs that require aggressive interventions. We aim to identify metabolic mechanisms associated with bacterial invasion, inflammatory cytokines, and biochemical markers in cases of fibrinous infectious pleural effusions in children with pneumonia. Pleural fluid metabolites were determined by 1H-nuclear magnetic resonance (NMR) spectroscopy. Metabolites contributed for the separation between fibrinous and non-fibrinous IPEs were identified using supervised partial least squares-discriminant analysis (Q2/R2 = 0...
February 13, 2019: Journal of Proteome Research
Frida Torell, Susanna Eketjäll, Helena Idborg, Per-Johan Jakobsson, Iva Gunnarsson, Elisabet Svenungsson, Johan Trygg
The aim of this study was to evaluate how the cytokine profiles differed between autoantibody based subgroups of systemic lupus erythematosus (SLE). SLE is a systemic autoimmune disease, characterized by periods of flares (active disease) and remission (inactive disease). The disease can affect many organ systems, e.g. skin, joints, kidneys, heart and the central nervous system (CNS). SLE patients often have an overproduction of cytokines, e.g. interferons, chemokines and interleukins. The high cytokine levels are part of the systemic inflammation which can lead to tissue injury...
February 11, 2019: Journal of Proteome Research
Anupam Banerjee, Yaakov Levy, Pralay Mitra
Protein backbone alternation due to insertion/deletion or mutation operation often results in a change of fundamental biophysical properties of proteins. The proposed work intends to encode the protein stability changes associated with single point deletions (SPDs) of amino acids in proteins. The encoding will help in the primary screening of detrimental backbone modifications before opting for expensive in-vitro experimentations. In the absence of any benchmark database documenting SPDs, we curate a dataset containing SPDs that lead to both folded conformations and unfolded state...
February 8, 2019: Journal of Proteome Research
Justin McKetney, Rosie Runde, Alexander S Hebert, Shahriar Salamat, Subhojit Roy, Joshua J Coon
The brain represents one of the most divergent and critical organs in the human body. Yet, it can be afflicted by a variety of neurodegenerative diseases specifically linked to aging, about which we lack a full biomolecular understanding of onset and progression, such as Alzheimer's Disease (AD). Here we provide a proteomic resource comprising nine functionally distinct sections from three individuals clinically diagnosed with AD, across a spectrum of disease progression. Using state-of-the-art mass spectrometry, we identify a core brain proteome that exhibits only small variance in expression, accompanied by a group of proteins that are highly differentially expressed in individual sections and broader regions...
February 8, 2019: Journal of Proteome Research
Brett M Noel, Steven B Ouellette, Laura Marholz, Deborah Dickey, Connor Navis, Tzu-Yi Yang, Vinh Nguyen, Sarah J Parker, David Bernlohr, Zohar Sachs, Laurie L Parker
Resistance to chemotherapy can occur through a wide variety of mechanisms. Resistance to tyrosine kinase inhibitors (TKIs) often arises from kinase mutations-however, "off-target" resistance occurs but is poorly understood. Previously, we established cell line resistance models for three TKIs used in chronic myeloid leukemia treatment, and found that resistance was not attributed entirely to failure of kinase inhibition. Here, we performed global, integrated proteomic and transcriptomic profiling of these cell lines to describe mechanisms of resistance at the protein and gene expression level...
February 7, 2019: Journal of Proteome Research
Yu Ye, Jun Zhu, Qiangyun Ai, Chengcheng Wang, Ming Liao, Huiying Fan
Outbreaks of porcine epidemic diarrhea virus (PEDV) have caused significant lethality rates in neonatal piglets, which pose a serious threat to the swine industry worldwide. Commercial vaccines available fail to protect against the emergence of high virulence of PEDV variants. Therefore, the endemic state of PEDV infection in suckling piglets highlights the urgent need for uncovering the molecular determinants of the disease pathogenesis. In this study, Stable Isotope Labeling by Amino acids in Cell culture (SILAC), combined with high performance liquid chromatography (HPLC)/tandem mass spectrometry, was performed to determine proteomic differences between PEDV-infected and mock-infected Vero cells at 18 h post-infection...
February 7, 2019: Journal of Proteome Research
Jan Muntel, Joanna Kirkpatrick, Roland Bruderer, Ting Huang, Olga Vitek, Alessandro Ori, Lukas Reiter
Label free quantification (LFQ) and isobaric labelling quantification (ILQ) are among the most popular protein quantification workflows in discovery proteomics. Here, we compared the TMT SPS/MS3 10-plex workflow to a label free single shot data-independent acquisition (DIA) workflow on a controlled sample set. The sample set consisted of ten samples derived from 10 biological replicates of mouse cerebelli spiked with the UPS2 protein standard in five different concentrations. For a fair comparison, we matched the instrument time for the two workflows...
February 6, 2019: Journal of Proteome Research
Damon H May, Kaipo Tamura, William Stafford Noble
Searching tandem mass spectra against a peptide database requires accurate knowledge of various experimental parameters, including machine settings and details of the sample preparation protocol. In some cases, such as in re-analysis of public data sets, this experimental metadata may be missing or inaccurate. We describe a method for automatically inferring the presence of various types of modifications, including stable-isotope and isobaric labeling and tandem mass tags, as well as enrichment of phosphorylated peptides, directly from a given set of mass spectra...
February 4, 2019: Journal of Proteome Research
Jimita Toraskar, Synnøve N Magnussen, Lars Hagen, Animesh Sharma, Linh Hoang, Geir Bjørkøy, Gunbjørg Svineng, Tonje S Steigedal
Extracellular vesicles are emerging as biomarkers in breast cancer. Our recent report suggested that an intracellular granular staining pattern of the extracellular matrix protein Nephronectin (NPNT) in breast tumor sections correlated with poor prognosis. Furthermore, the results showed that NPNT is localized in extracellular vesicles derived from mouse breast cancer cells. In this study we performed proteomic analysis which reveals that several proteins, including tumor promoting molecules are differentially expressed in the cargo of small extracellular vesicles (sEVs) upon NPNT expression in mouse breast cancer cells...
February 1, 2019: Journal of Proteome Research
Indranil Sarkar, Adriana Zardini Buzatto, Ravendra Garg, Liang Li, Sylvia van Drunen Littel-van den Hurk
Respiratory syncytial virus (RSV) is a significant cause of mortality and morbidity in infants, elderly, immunocompromised individuals and patients with congenital heart diseases. Despite extensive efforts, a vaccine against RSV is still not available. We have previously reported the development of a subunit vaccine (ΔF/TriAdj) composed by a truncated version of the fusion protein (ΔF) and a polymer-based combination adjuvant (TriAdj). In the present study, we compared inflammatory responses of ΔF/TriAdj-vaccinated and unvaccinated mice following intranasal challenge with RSV...
February 1, 2019: Journal of Proteome Research
Ting Zhang, Qi Zhao, Xuerong Xiao, Rui Yang, Dandan Hu, Xu Zhu, Frank J Gonzalez, Fei Li
Hyperlipidemia, characterized by high serum lipids, is a risk factor for cardiovascular disease. Recent studies have identified an important role for celastrol, a proteasome inhibitor isolated from Tripterygium wilfordii Hook. F., in obesity-related metabolic disorders. However, the exact influences of celastrol on lipid metabolism remains largely unknown. Celastrol inhibited the terminal differentiation of 3T3-L1 adipocytes, and decreased the levels of triglycerides in wild-type mice. Lipidomics analysis revealed that celastrol increased the metabolism of lysophosphatidylcholines (LPCs), phosphatidylcholines (PCs), sphingomyelins (SMs), and phosphatidylethanolamines (PEs)...
February 1, 2019: Journal of Proteome Research
Dilys T H Leung, Adam Rainczuk, Trang Nguyen, Andrew Stephens, John Silke, Peter J Fuller, Simon Chu
Ovarian granulosa cell tumors (GCT) are hormonally-active cancers characterized by indolent growth and late, invasive relapse. No therapies have yet proven to be efficacious. We previously reported that inhibition of the anti-apoptotic X-linked inhibitor of apoptosis protein (XIAP) removes transrepression of the pro-proliferative nuclear receptor, peroxisome proliferator-activated receptor (PPAR)-γ, in a GCT-derived cell line, KGN. Both PPARγ and XIAP are overexpressed in human GCT. Inhibition of XIAP with restoration of PPARγ signaling using a SMAC-mimetic (Compound A; CmpdA) and rosiglitazone (RGZ)/retinoic acid (RA), respectively, reduced cell proliferation and induced apoptosis in the KGN cells...
February 1, 2019: Journal of Proteome Research
Shimin Chen, Charles Yang, Melanie L Downs
Soybean is one of the major allergenic foods in many countries. Soybean is commonly processed into different types of soy ingredients to achieve desired properties. The processing, however, may affect the protein profiles and protein structure, thus affecting the detection of soy proteins. Mass spectrometry is a potential alternative to the traditional immunoassays for the detection of soy-derived ingredients in foods. This study aims to develop an LC-MS/MS method that uniformly detects different types of soy-derived ingredients...
February 1, 2019: Journal of Proteome Research
Mak A Saito, Erin M Bertrand, Megan E Duffy, David A Gaylord, Noelle A Held, William Judson Hervey, Robert L Hettich, Pratik Jagtap, Michael G Janech, Danie B Kinkade, Dasha Leary, Matthew McIlvin, Eli Moore, Robert Morris, Benjamin A Neely, Brook Nunn, Jaclyn K Saunders, Adam Shepherd, Nicholas Symmonds, David Walsh
Ocean metaproteomics is an emerging field enabling discoveries about marine microbial communities and their impact on global biogeochemical processes. Recent ocean metaproteomic studies have provided insight into microbial nutrient transport, co-limitation of carbon fixation, the metabolism of microbial biofilms, and dynamics of carbon flux in marine ecosystems. Future methodological developments could provide new capabilities such as characterizing long-term ecosystem changes, biogeochemical reaction rates, and in situ stoichiometries...
January 31, 2019: Journal of Proteome Research
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