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Journal of Proteome Research

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https://www.readbyqxmd.com/read/28196416/blood-proteomic-profiling-in-inherited-attrm-and-acquired-attrwt-forms-of-transthyretin-associated-cardiac-amyloidosis
#1
Gloria G Chan, Clarissa M Koch, Lawreen H Connors
Transthyretin-associated forms of cardiac amyloidosis are fatal protein misfolding diseases that can be inherited (ATTRm) or acquired (ATTRwt). An accurate diagnosis of ATTR amyloidosis can be challenging as biopsy evidence, usually from the affected organ, is required. Precise biomarkers for ATTR disease identification and monitoring are undiscovered, disease-specific therapeutic options are needed, and the current understanding of ATTR molecular pathogenesis is limited. The aim of this study was to investigate and compare the serum proteomes in ATTRm and ATTRwt cardiac amyloidosis to identify differentially expressed blood proteins that were disease-specific...
February 23, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28166636/cartilaginous-metabolomic-study-reveals-potential-mechanisms-of-osteophyte-formation-in-osteoarthritis
#2
Zhongwei Xu, Tingmei Chen, Jiao Luo, Shijia Ding, Sichuan Gao, Jian Zhang
Osteophyte is one of the inevitable consequences of progressive osteoarthritis with the main characteristics of cartilage degeneration and endochondral ossification. The pathogenesis of osteophyte formation is not fully understood to date. In this work, metabolomic approaches were employed to explore potential mechanisms of osteophyte formation by detecting metabolic variations between extracts of osteophyte cartilage tissues (n = 32) and uninvolved control cartilage tissues (n = 34), based on the platform of ultraperformance liquid chromatography tandem quadrupole time-of-flight mass spectrometry, as well as the use of multivariate statistic analysis and univariate statistic analysis...
February 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28217993/assessment-of-label-free-quantification-in-discovery-proteomics-and-impact-of-technological-factors-and-natural-variability-of-protein-abundance
#3
Mhd Rami Al Shweiki, Susann Mönchgesang, Petra Majovsky, Domenika Thieme, Diana Trutschel, Wolfgang Hoehenwarter
We evaluated the state of label-free discovery proteomics focusing especially on technological contributions and contributions of naturally occurring differences in protein abundance to the inter-sample variability in protein abundance estimates in this highly peptide-centric technology. First, the performance of popular quantitative proteomics software, Proteome Discoverer, Scaffold, MaxQuant and Progenesis QIP was benchmarked using their default parameters and some modified settings. Beyond this the inter- sample variability in protein abundance estimates was decomposed into variability introduced by the entire technology itself and variable protein amounts inherent to individual plants of the Arabidopsis thaliana Col-0 accession...
February 20, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28199111/parallel-comparison-of-n-linked-glycopeptide-enrichment-techniques-reveals-extensive-glycoproteomic-analysis-of-plasma-enabled-by-sax-erlic
#4
Sarah M Totten, Christa L Feasley, Abel Bermudez, Sharon J Pitteri
Protein glycosylation is of increasing interest due to its important roles in protein function and aberrant expression with disease. Characterizing protein glycosylation remains analytically challenging due to its low abundance, ion suppression issues, and microheterogeneity at glycosylation sites, especially in complex samples such as human plasma. In this study, the utility of three common N-linked glycopeptide enrichment techniques is compared using human plasma. By analysis on an LTQ-Orbitrap Elite mass spectrometer, electrostatic repulsion hydrophilic interaction liquid chromatography using strong anion exchange solid-phase extraction (SAX-ERLIC) provided the most extensive N-linked glycopeptide enrichment when compared with multilectin affinity chromatography (M-LAC) and Sepharose-HILIC enrichments...
February 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28176526/maldi-versus-esi-the-impact-of-the-ion-source-on-peptide-identification
#5
Wiebke Maria Nadler, Dietmar Waidelich, Alexander Kerner, Sabrina Hanke, Regina Berg, Andreas Trumpp, Christoph Rösli
For mass spectrometry-based proteomic analyses, electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) are the commonly used ionization techniques. To investigate the influence of the ion source on peptide detection in large-scale proteomics, an optimized GeLC/MS workflow was developed and applied either with ESI/MS or with MALDI/MS for the proteomic analysis of different human cell lines of pancreatic origin. Statistical analysis of the resulting data set with more than 72 000 peptides emphasized the complementary character of the two methods, as the percentage of peptides identified with both approaches was as low as 39%...
February 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28166638/the-peptideatlas-of-the-domestic-laying-hen
#6
James McCord, Zhi Sun, Eric W Deutsch, Robert L Moritz, David C Muddiman
Proteomics-based biological research is greatly expanded by high-quality mass spectrometry studies, which are themselves enabled by access to quality mass spectrometry resources, such as high-quality curated proteome data repositories. We present a PeptideAtlas for the domestic chicken, containing an extensive and robust collection of chicken tissue and plasma samples with substantial value for the chicken proteomics community for protein validation and design of downstream targeted proteome quantitation. The chicken PeptideAtlas contains 6646 canonical proteins at a protein FDR of 1...
February 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28145113/exploring-the-links-between-diet-and-health-in-an-irish-cohort-a-lipidomic-approach
#7
Aoife O'Gorman, Helena Gibbons, Miriam F Ryan, Eileen R Gibney, Michael J Gibney, Gary S Frost, Helen M Roche, Lorraine Brennan
Epidemiology and clinical studies provide clear evidence of the complex links between diet and health. To understand these links, reliable dietary assessment methods are pivotal. Biomarkers have emerged as more objective measures of intake compared with traditional dietary assessment methods. However, there are only a limited number of putative biomarkers of intake successfully identified and validated. The use of biomarkers that reflect food intake to examine diet related diseases represents the next step in biomarker research...
February 13, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28186774/quantitative-map-of-%C3%AE-lactone-induced-virulence-regulation
#8
Joanna Krysiak, Matthias Stahl, Jan Vomacka, Christian Fetzer, Markus Lakemeyer, Anja Fux, Stephan A Sieber
β-Lactones have recently been introduced as the first selective ClpP inhibitors that attenuate virulence of both sensitive Staphylococcus aureus and multiresistant strains (MRSA). Although previous knockout studies showed that ClpP is essential for S. aureus alpha-toxin production, a link between β-lactone inhibition and molecular virulence mechanisms has been lacking so far. We here perform a chemical-proteomic approach to elucidate antivirulence pathways. First, we demonstrate by gel-free activity-based protein profiling that ClpP is the predominant target of β-lactones...
February 10, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28152313/analysis-of-stage-specific-protein-expression-during-babesia-bovis-development-within-female-rhipicephalus-microplus
#9
Wendell C Johnson, Naomi S Taus, Kathryn E Reif, Gamila A R Bohaliga, Lowell S Kappmeyer, Massaro W Ueti
Arthropod-borne protozoan pathogens have a complex life cycle that includes asexual reproduction of haploid stages in mammalian hosts and the development of diploid stages in invertebrate hosts. The ability of pathogens to invade, survive, and replicate within distinct cell types is required to maintain their life cycle. In this study, we describe a comparative proteomic analysis of a cattle pathogen, Babesia bovis, during its development within the mammalian and tick hosts with the goal of identifying cell-surface proteins expressed by B...
February 9, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28121444/whole-proteome-peptide-microarrays-for-profiling-autoantibody-repertoires-within-multiple-sclerosis-and-narcolepsy
#10
Arash Zandian, Björn Forsström, Anna Häggmark-Månberg, Jochen M Schwenk, Mathias Uhlén, Peter Nilsson, Burcu Ayoglu
The underlying molecular mechanisms of autoimmune diseases are poorly understood. To unravel the autoimmune processes across diseases, comprehensive and unbiased analyses of proteins targets recognized by the adaptive immune system are needed. Here we present an approach starting from high-density peptide arrays to characterize autoantibody repertoires and to identify new autoantigens. A set of ten plasma and serum samples from subjects with multiple sclerosis, narcolepsy, and without any disease diagnosis were profiled on a peptide array representing the whole proteome, hosting 2...
February 9, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28088864/integrated-high-throughput-multiomics-platform-enables-data-driven-construction-of-cellular-responses-and-reveals-global-drug-mechanisms-of-action
#11
Jeremy L Norris, Melissa A Farrow, Danielle B Gutierrez, Lauren D Palmer, Nicole Muszynski, Stacy D Sherrod, James C Pino, Jamie L Allen, Jeffrey M Spraggins, Alex L R Lubbock, Ashley Jordan, William Burns, James C Poland, Carrie Romer, M Lisa Manier, Yuan-Wei Nei, Boone M Prentice, Kristie L Rose, Salisha Hill, Raf Van de Plas, Tina Tsui, Nathaniel M Braman, M Ray Keller, Stacey A Rutherford, Nichole Lobdell, Carlos F Lopez, D Borden Lacy, John A McLean, John P Wikswo, Eric P Skaar, Richard M Caprioli
An understanding of how cells respond to perturbation is essential for biological applications; however, most approaches for profiling cellular response are limited in scope to pre-established targets. Global analysis of molecular mechanism will advance our understanding of the complex networks constituting cellular perturbation and lead to advancements in areas, such as infectious disease pathogenesis, developmental biology, pathophysiology, pharmacology, and toxicology. We have developed a high-throughput multiomics platform for comprehensive, de novo characterization of cellular mechanisms of action...
February 9, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28171727/multiplexed-phosphoproteomic-profiling-using-titanium-dioxide-and-immuno-affinity-enrichments-reveals-complementary-phosphorylation-events
#12
Anthony P Possemato, Joao A Paulo, Daniel Mulhern, Ailan Guo, Steven P Gygi, Sean A Beausoleil
A comprehensive view of protein phosphorylation remains an unmet challenge in the field of cell biology. Mass spectrometry-based proteomics is one of the most promising approaches for identifying thousands of phosphorylation events in a single experiment, yet the full breadth of the phosphoproteome has yet to be elucidated. In this report, we examined the complementarity of two methods for phosphopeptide enrichment based on either titanium dioxide (TiO2) enrichment or phosphorylation motif-specific immuno-affinity precipitation (IAP) with four different antibodies...
February 7, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28168879/head-and-neck-squamous-cell-carcinoma-metabolism-draws-on-glutaminolysis-and-stemness-is-specifically-regulated-by-glutaminolysis-via-aldehyde-dehydrogenase
#13
Pachiyappan Kamarajan, Thekkelnaycke M Rajendiran, Jason Kinchen, Mercedes Bermúdez, Theodora Danciu, Yvonne Lorraine Kapila
Cancer cells use alternate energetic pathways, however cancer stem cell (CSC) metabolic energetic pathways are unknown. The purpose of this study was to define the metabolic characteristics of head and neck cancer at different points of its pathogenesis with a focus on its CSC compartment. UPLC-MS/MS-profiling and GC-MS-validation studies of human head and neck cancer tissue, saliva, and plasma, were used in conjunction with in vitro and in vivo models to carry out this investigation. We identified metabolite biomarker panels that distinguish head and neck cancer from healthy controls, and confirmed involvement of glutamate and glutaminolysis...
February 7, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28168878/network-marker-selection-for-untargeted-lc-ms-metabolomics-data
#14
Qingpo Cai, Jessica A Alvarez, Jian Kang, Tianwei Yu
Untargeted metabolomics using high-resolution liquid chromatography - mass spectrometry (LC-MS) is becoming one of the major areas of high-throughput biology. Functional analysis, i.e. analyzing the data based on metabolic pathways or the genome-scale metabolic network, is critical in feature selection and interpretation of metabolomics data. One of the main challenges in the functional analyses is the lack of the feature identity in the LC-MS data itself. By matching mass-to-charge ratio (m/z) values of the features to theoretical values derived from known metabolites, some features can be matched to one or more known metabolites...
February 7, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28166632/metabolomics-based-elucidation-of-active-metabolic-pathways-in-erythrocytes-and-hsc-derived-reticulocytes
#15
Anubhav Srivastava, Krystal J Evans, Anna Elizabeth Sexton, Louis Schofield, Darren John Creek
A detailed analysis of the metabolic state of human stem cell derived erythrocytes allowed us to characterize the existence of active metabolic pathways in younger reticulocytes and compare them to mature erythrocytes. Using high resolution LC-MS based, untargeted metabolomics, we found that reticulocytes had a comparatively much richer repertoire of metabolites, which spanned a range of metabolite classes. An untargeted metabolomics analysis using stable isotope-labelled glucose showed that only glycolysis and the pentose phosphate pathway actively contributed to the biosynthesis of metabolites in erythrocytes, and these pathways were upregulated in reticulocytes...
February 7, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28112948/mass-spectrometry-based-method-to-quantify-in-parallel-tau-and-amyloid-%C3%AE-1-42-in-csf-for-the-diagnosis-of-alzheimer-s-disease
#16
Gwënaël Pottiez, Li Yang, Tessandra Stewart, Ning Song, Patrick Aro, Douglas R Galasko, Joseph F Quinn, Elaine R Peskind, Min Shi, Jing Zhang
Alzheimer's disease (AD), the most common form of dementia, afflicts about 50 million people worldwide. Currently, AD diagnosis is primarily based on psychological evaluation and can only be confirmed post-mortem. Reliable and objective biomarkers for prognosis and diagnosis have been sought for years. Together, tau and amyloid β 1-42 (Aβ42) in cerebrospinal fluid (CSF) have been shown to provide good diagnostic sensitivity and specificity. Additionally, phosphorylated forms of tau, such as tau pS181, have also shown promising results...
February 7, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28099032/pathogenicity-genes-in-ustilaginoidea-virens-revealed-by-a-predicted-protein-protein-interaction-network
#17
Kang Zhang, Yuejiao Li, Tengjiao Li, Zhi-Gang Li, Tom Hsiang, Ziding Zhang, Wenxian Sun
Rice false smut, caused by Ustilaginoidea virens, produces significant losses in rice yield and grain quality and has recently emerged as one of the most important rice diseases worldwide. Despite its importance in rice production, relatively few studies have been conducted to illustrate the complex interactome and the pathogenicity gene interactions. Here a protein-protein interaction network of U. virens was built through two well-recognized approaches, interolog- and domain-domain interaction-based methods...
February 7, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28164708/expanding-proteome-coverage-with-charge-ordered-parallel-ion-analysis-chopin-combined-with-broad-specificity-proteolysis
#18
Simon Davis, Philip D Charles, Lin He, Peter Mowlds, Benedikt M Kessler, Roman Fischer
The "deep" proteome has been accessible by mass spectrometry for some time. However, the number of proteins identified in cells of the same type has plateaued at ~8,000-10,000 without ID transfer from reference proteomes/data. Moreover, limited sequence coverage hampers the discrimination of protein isoforms when using trypsin as standard protease. Multi-enzyme approaches appear to improve sequence coverage and subsequent isoform discrimination. Here, we expanded proteome and protein sequence coverage in MCF-7 breast cancer cells to an as yet unmatched depth, by employing a workflow that addresses current limitations in deep proteome analysis at multiple stages: We used i) Gel-aided sample preparation (GASP) and combined trypsin/elastase digests to increase peptide orthogonality, ii) concatenated high pH pre-fractionation and iii) CHarge Ordered Parallel Ion aNalysis (CHOPIN)- available on an Orbitrap Fusion (Lumos) mass spectrometer- to achieve 57% median protein sequence coverage in 13,728 protein groups (8,949 Unigene IDs) in a single cell line...
February 6, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28164707/discovery-of-novel-antimicrobial-peptides-from-varanus-komodoensis-komodo-dragon-by-large-scale-analyses-and-de-novo-assisted-sequencing-using-electron-transfer-dissociation-mass-spectrometry
#19
Barney M Bishop, Melanie L Juba, Paul S Russo, Megan Devine, Stephanie M Barksdale, Shaylyn Scott, Robert Settlage, Pawel Michalak, Kajal Gupta, Kent Vliet, Joel M Schnur, Monique L van Hoek
Komodo dragons are the largest living lizards and are the apex predators in their environs. They endure numerous strains of pathogenic bacteria in their saliva and recover from wounds inflicted by other dragons, reflecting the inherent robustness of their innate immune defense. We have employed a custom bioprospecting approach combining partial de novo peptide sequencing with transcriptome assembly to identify cationic antimicrobial peptides from Komodo dragon plasma. Through these analyses, we identified 48 novel potential cationic antimicrobial peptides...
February 6, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28161958/comprehensive-metaboproteomics-of-burkitt-s-and-diffuse-large-b-cell-lymphoma-cell-lines-and-primary-tumor-tissues-reveals-distinct-differences-in-pyruvate-content-and-metabolism
#20
Philipp Schwarzfischer, Joerg Reinders, Katja Dettmer, Karsten Kleo, Lora Dimitrova, Michael Hummel, Maren Feist, Dieter Kube, Monika Szczepanowski, Wolfram Klapper, Franziska Taruttis, Julia C Engelmann, Rainer Spang, Wolfram Gronwald, Peter J Oefner
Burkitt's lymphoma (BL) and diffuse large B-cell lymphoma (DLBCL) are pathologically and clinically distinct subtypes of aggressive non-Hodgkin B-cell lymphoma. To learn more about their biology, we employed metabolomic and proteomic methods to study both established cell lines as well as cryopreserved and formalin-fixed paraffin-embedded (FFPE) tissue sections of BL and DLBCL. Strikingly, NMR analyses revealed DLBCL cell lines to produce and secrete significantly (padj=1.72 x 10-22) more pyruvic acid than BL cell lines...
February 6, 2017: Journal of Proteome Research
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