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Journal of Proteome Research

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https://www.readbyqxmd.com/read/29148801/neuropeptidomics-of-the-bed-bug-cimex-lectularius
#1
Reinhard Predel, Susanne Neupert, Christian Derst, Klaus Reinhardt, Christian Wegener
The bed bug Cimex lectularius is a globally distributed human ectoparasite with fascinating biology. It has recently acquired resistance against a broad range of insecticides, causing a worldwide increase in bed bug infestations. The recent annotation of the bed bug genome revealed a full complement of neuropeptide and neuropeptide receptor genes in this species. With regard to the biology of C. lectularius, neuropeptide signalling is especially interesting since it regulates feeding, diuresis, digestion as well as reproduction, and also provides potential new targets for chemical control...
November 17, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29148792/proteomic-markers-of-the-functional-sperm-population-in-bovines-1-comparison-of-low-and-high-density-spermatozoa-following-cryopreservation
#2
Olivier D'Amours, Gilles Frenette, Sylvie Bourassa, Ezequiel Calvo, Patrick Blondin, Robert Sullivan
Mammalian semen contains a heterogeneous population of sperm cells. This heterogeneity results from variability in the complex processes of cell differentiation in the testis, biochemical modifications undergone by spermatozoa during transit along the male reproductive tract, interactions with secretions from accessory sex glands at ejaculation, and, in the context of reproductive technologies, in the ability of ejaculated spermatozoa to resist damage associated with freeze-thaw procedures. When submitted to density gradient centrifugation, ejaculated spermatozoa distribute themselves into two distinct populations: a low-density population characterized by low motility parameters, and a high-density population with high motility characteristics...
November 17, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29083190/marked-differences-in-the-submandibular-salivary-proteome-between-sardinian-alcohol-preferring-and-sardinian-alcohol-non-preferring-rats-revealed-by-an-integrated-top-down-bottom-up-proteomic-platform
#3
Tiziana Cabras, Alfredo D'Alessandro, Simone Serrao, Raffaella Isola, Federica Iavarone, Federica Vincenzoni, Giancarlo Colombo, Jörgen Ekström, Irene Messana, Massimo Castagnola
Sardinian alcohol-preferring (sP) and Sardinian alcohol-non preferring (sNP) rats have been selectively bred for opposite alcohol preference and consumption. Aiming to verify possible differences at the proteomics level between sP and sNP rats, we investigated the salivary proteome by a a liquid chromatography-mass spectrometry top-down-bottom-up integrated approach. For this purpose, submandibular saliva was collected from alcohol-naive sP and sNP rats under isoprenaline stimulation. A total of 200 peptides and proteins were detected and quantified in the two rat lines, 149 of which were characterized in their naturally occurring structure...
November 16, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29139296/differential-content-of-proteins-mrnas-and-mirnas-suggests-that-mdsc-and-their-exosomes-may-mediate-distinct-immune-suppressive-functions
#4
Lucia Geis-Asteggiante, Ashton T Belew, Virginia K Clements, Nathan J Edwards, Suzanne Ostrand-Rosenberg, Nagib M El-Sayed, Catherine Fenselau
Myeloid-derived suppressor cells (MDSC) are immature myeloid cells that accumulate in the circulation and the tumor microenvironment of most cancer patients. There, MDSC suppress both adaptive and innate immunity, hindering immunotherapies. The inflammatory milieu often present in cancers facilitates MDSC suppressive activity, causing aggressive tumor progression and metastasis. MDSC from tumor-bearing mice release exosomes, which carry biologically active proteins and mediate some of the immunosuppressive functions characteristic of MDSC...
November 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29116813/tio2-with-tandem-fractionation-taft-an-approach-for-rapid-deep-reproducible-and-high-throughput-phosphoproteome-analysis
#5
Liangliang Ren, Chaoying Li, Wenli Shao, Weiran Lin, Fuchu He, Ying Jiang
Mass-spectrometry-based phosphoproteomic workflows traditionally require efficient prefractionation and enrichment of phosphopeptides to gain an in-depth, global, and unbiased systematic investigation of phosphoproteome. Here we present TiO2 with tandem fractionation (TAFT) approach, which combines titanium dioxide (TiO2) enrichment and tandem high-pH reverse-phase (HpRP) for phosphoproteome analysis in a high-throughput manner; the entire workflow takes only 3 h to complete without laborious phosphopeptide preparation...
November 15, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29135266/fast-metabolite-identification-in-nuclear-magnetic-resonance-metabolomic-studies-statistical-peak-sorting-and-peak-overlap-detection-for-more-reliable-database-queries
#6
Pablo A Hoijemberg, Istvan Pelczer
A lot of time is spent by researchers in the identification of metabolites in NMR-based metabolomic studies. The usual metabolite identification starts employing public or commercial databases to match chemical shifts thought to belong to a given compound. Statistical total correlation spectroscopy (STOCSY), in use for more than a decade, speeds the process by finding statistical correlations among peaks, being able to create a better peak list as input for the database query. However, the (normally not automated) analysis becomes challenging due to the intrinsic issue of peak overlap, where correlations of more than one compound appear in the STOCSY trace...
November 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29115832/improved-prediction-of-bovine-leucocyte-antigens-bola-presented-ligands-by-use-of-mass-spectrometry-determined-ligand-and-in-vitro-binding-data
#7
Morten Nielsen, Tim Connelley, Nicola Ternette
Peptide binding to MHC class I molecules is the single most selective step in antigen presentation and the strongest single correlate to peptide cellular immunogenicity. The cost of experimentally characterizing the rules of peptide presentation for a given MHC-I molecule is extensive, and predictors of peptide-MHC interactions constitute an attractive alternative. Recently, an increasing amount of MHC presented peptides identified by mass spectrometry (MS ligands) has been published. Handling and interpretation of MS ligand data is, in general, challenging due to the polyspecificity nature of the data...
November 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29111762/metabolomics-and-lipidomics-profiling-of-a-combined-mitochondrial-plus-endoplasmic-reticulum-fraction-of-human-fibroblasts-a-robust-tool-for-clinical-studies
#8
Charlotte Veyrat-Durebex, Cinzia Bocca, Stéphanie Chupin, Judith Kouassi Nzoughet, Gilles Simard, Guy Lenaers, Pascal Reynier, Hélène Blasco
Mitochondria and endoplasmic reticulum (ER) are physically and functionally connected. This close interaction, via mitochondria-associated membranes, is increasingly explored and supports the importance of studying these two organelles as a whole. Metabolomics and lipidomics are powerful approaches for the exploration of metabolic pathways that may be useful to provide deeper information on these organelles' functions, dysfunctions, and interactions. We developed a quick and simple experimental procedure for the purification of a mitochondria-ER fraction from human fibroblasts...
November 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29067805/gentle-introduction-to-the-statistical-foundations-of-false-discovery-rate-in-quantitative-proteomics
#9
Thomas Burger
The vocabulary of theoretical statistics can be difficult to embrace from the viewpoint of computational proteomics research, even though the notions it conveys are essential to publication guidelines. For example, "adjusted p-values", "q-values", and "false discovery rates" are essentially similar concepts, whereas "false discovery rate" and "false discovery proportion" must not be confused, even though "rate" and "proportion" are related in everyday language. In the interdisciplinary context of proteomics, such subtleties may cause misunderstandings...
November 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28976774/proteomic-analysis-of-extracellular-hmgb1-identifies-binding-partners-and-exposes-its-potential-role-in-airway-epithelial-cell-homeostasis
#10
Sharon L Wong, Joyce To, Jerran Santos, Venkata Sita Rama Raju Allam, John P Dalton, Steven P Djordjevic, Sheila Donnelly, Matthew P Padula, Maria B Sukkar
The release of damage-associated molecular patterns (DAMPs) by airway epithelial cells is believed to play a crucial role in the initiation and development of chronic airway conditions such as asthma and chronic obstructive pulmonary disease (COPD). Intriguingly, the classic DAMP high-mobility group box-1 (HMGB1) is detected in the culture supernatant of airway epithelial cells under basal conditions, indicating a role for HMGB1 in the regulation of epithelial cellular and immune homeostasis. To gain contextual insight into the potential role of HMGB1 in airway epithelial cell homeostasis, we used the orthogonal and complementary methods of high-resolution clear native electrophoresis, immunoprecipitation, and pull-downs coupled to liquid chromatography-tandem mass spectrometry (LC-MS/MS) to profile HMGB1 and its binding partners in the culture supernatant of unstimulated airway epithelial cells...
November 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29131649/characterization-of-proteomes-extracted-through-collagen-based-stable-isotope-and-radiocarbon-dating-methods
#11
Caroline Wadsworth, Michael Buckley
Isotope analyses on "collagen" extracted from ancient bone have been routinely used for dietary and chronological inferences worldwide for decades. These methods involve the decalcification of biomineralized tissues with acid, often followed by processes to remove exogenous contaminants, and then gelatinization of what is often described as the "collagen" fraction. However, little is known about the relative content of collagen to the many other noncollagenous proteins (NCPs) potentially present. Some of these NCPs have great longevity in ancient bone, and some, for example, fetuin-A, are useful for obtaining better taxonomic information than collagen...
November 13, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29131639/proteomic-characterization-of-transcription-and-splicing-factors-associated-with-a-metastatic-phenotype-in-colorectal-cancer
#12
Sofia Torres, Irene Garcia-Palmero, Consolación Marin-Vicente, Ruben A Bartolome, Eva Calviño, María Jesús Fernandez-Aceñero, J Ignacio Casal
We investigated new transcription and splicing factors associated with the metastatic phenotype in colorectal cancer. A concatenated tandem array of consensus transcription factors (TFs)-response elements was used to pull down nuclear extracts in two different pairs of colorectal cancer cells, KM12SM/KM12C and SW620/480, genetically-related but differing in metastatic ability. Proteins were analyzed by label-free LC-MS and quantified with MaxLFQ. We found 240 proteins showing a significant dysregulation in highly-metastatic KM12SM cells relative to non-metastatic KM12C cells and 257 proteins in metastatic SW620 versus SW480...
November 13, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29130306/evaluating-in-vitro-culture-medium-of-gut-microbiome-with-orthogonal-experimental-design-and-metaproteomics-approach
#13
Leyuan Li, Xu Zhang, Zhibin Ning, Janice Mayne, Jasmine I Moore, James Butcher, Cheng-Kang Chiang, David R Mack, Alain Stintzi, Daniel Figeys
In vitro culture-based approaches are time- and cost-effective solutions for rapidly evaluating the effects of drugs or natural compounds against microbiomes. The nutritional composition of the culture medium is an important determinant for effectively maintaining the gut microbiome in vitro. This study combines orthogonal experimental design and a metaproteomics approach to obtain functional insights into the effects of different medium components on the microbiome. Our results show that the metaproteomic profile respond differently to medium components, including inorganic salts, bile salts, mucin and short chain fatty acids...
November 13, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29130300/psite-amino-acid-confidence-evaluation-for-quality-control-of-de-novo-peptide-sequencing-and-modification-site-localization
#14
Hao Yang, Hao Chi, Wen-Jing Zhou, Wen-Feng Zeng, Chao Liu, Rui-Min Wang, Zhao-Wei Wang, Xiu-Nan Niu, Zhen-Lin Chen, Si-Min He
MS-based de novo peptide sequencing has been improved remarkably with significant development of mass spectrometry and computational approaches, but still lacks quality control methods. Here we proposed a novel algorithm pSite to evaluate the confidence of each amino acid rather than the full-length peptides obtained by de novo peptide sequencing. A semi-supervised learning approach was used to discriminate correct amino acids from random ones and then an expectation-maximization algorithm was used to adaptively control the false amino-acid rate (FAR)...
November 13, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29110486/impact-of-detergents-on-membrane-protein-complex-isolation
#15
Yu-Chen Lee, Jenny Arnling Bååth, Ryan M Bastle, Sonali Bhattacharjee, Mary Jo Cantoria, Mark Dornan, Enrique Gamero-Estevez, Lenzie Ford, Lenka Halova, Jennifer Kernan, Charlotte Kürten, Siran Li, Jerahme Martinez, Nalani Sachan, Medoune Sarr, Xiwei Shan, Nandhitha Subramanian, Keith Rivera, Darryl Pappin, Sue-Hwa Lin
Detergents play an essential role during the isolation of membrane protein complexes. Inappropriate use of detergents may affect the native fold of the membrane proteins, their binding to antibodies, or their interaction with partner proteins. Here we used cadherin-11 (Cad11) as an example to examine the impact of detergents on membrane protein complex isolation. We found that mAb 1A5 could immunoprecipitate Cad11 when membranes were solubilized by dodecyl maltoside (DDM) but not by octylglucoside, suggesting that octylglucoside interferes with Cad11-mAb 1A5 interaction...
November 13, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29129073/stage-dependence-cell-origin-independence-and-prognostic-capacity-of-serum-glycan-fucosylation-%C3%AE-1-4-branching-%C3%AE-1-6-branching-and-%C3%AE-2-6-sialylation-in-cancer
#16
Shadi Ferdosi, Douglas S Rehder, Paul Maranian, Erik P Castle, Thai H Ho, Harvey I Pass, Daniel W Cramer, Karen S Anderson, Lei Fu, David E C Cole, Tao Le, Xifeng Wu, Chad R Borges
Glycans represent a promising but only marginally accessed source of cancer markers. We previously reported the development of a molecularly bottom-up approach to plasma/serum (P/S) glycomics based on glycan linkage analysis that captures features such as α2-6 sialylation, β1-6 branching, and core fucosylation as single analytical signals. Based on the behavior of P/S glycans established to date, we hypothesized that the alteration of P/S glycans observed in cancer would be independent of the tissue in which the tumor originated yet exhibit stage dependence that varied little between cancers classified on the basis of tumor origin...
November 12, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29129081/identification-of-mature-atherosclerotic-plaque-proteome-signatures-using-data-independent-acquisition-mass-spectrometry
#17
Nicole Hansmeier, Josef Buttigieg, Pankaj Kumar, Shaneen Pelle, Kyoo Yoon Choi, David Kopriva, Tzu-Chiao Chao
Atherosclerosis is a chronic inflammatory disease with complex pathobiology and one of the most common causes of cardiovascular events. The process is characterized by complex vascular remodeling processes that require the actions of numerous proteins. The composition of atherosclerotic plaque is increasingly recognized as a major factor governing the occurrence of cardiovascular or neurological symptoms. In order to gain deeper insights in the composition of atherosclerotic plaques, we created quantitative proteome profiles of advanced plaque tissues of six male patients undergoing carotid endarterectomy for stroke prevention...
November 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29124938/quality-assessments-of-long-term-quantitative-proteomic-analysis-of-breast-cancer-xenograft-tissues
#18
Jian-Ying Zhou, Lijun Chen, Bai Zhang, Yuan Tian, Tao Liu, Stefani N Thomas, Li Chen, Michael Schnaubelt, Emily Boja, Tara Hiltke, Christopher R Kinsinger, Henry Rodriguez, Sherri R Davies, Shunqiang Li, Jacqueline E Snider, Petra Erdmann-Gilmore, David L Tabb, R Reid Townsend, Matthew J Ellis, Karin D Rodland, Richard D Smith, Steven A Carr, Zhen Zhang, Daniel W Chan, Hui Zhang
Clinical proteomics requires large-scale analysis of human specimens to achieve statistical significance. In this study, we evaluated the long-term reproducibility of an iTRAQ (isobaric tags for relative and absolute quantification)-based quantitative proteomics strategy using one channel for reference across all samples in different iTRAQ sets. A total of 148 liquid chromatography tandem mass spectrometric (LC-MS/MS) analyses were completed, generating 6 two-dimensional (2D) LC-MS/MS datasets for human-in-mouse breast cancer xenograft tissues representative of basal and luminal subtypes...
November 10, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29098862/proteomic-analyses-of-cysteine-redox-in-high-fat-fed-and-fasted-mouse-livers-implications-for-liver-metabolic-homeostasis
#19
Yixing Li, Zupeng Luo, Xilong Wu, Jun Zhu, Kai Yu, Yi Jin, Zhiwang Zhang, Shuhong Zhao, Lei Zhou
Intensive oxidative stress occurs during high-fat-diet-induced hepatic fat deposition, suggesting a critical role for redox signaling in liver metabolism. Intriguingly, evidence shows that fasting could also result in redox-profile changes largely through reduced oxidant or increased antioxidant levels. However, a comprehensive landscape of redox-modified hepatic substrates is lacking, thereby hindering our understanding of liver metabolic homeostasis. We employed a proteomic approach combining iodoacetyl tandem mass tag and nanoliquid chromatography tandem mass spectrometry to quantitatively probe the effects of high-fat feeding and fasting on in vivo redox-based cysteine modifications...
November 10, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29083192/tip-based-fractionation-of-batch-enriched-phosphopeptides-facilitates-easy-and-robust-phosphoproteome-analysis
#20
Alireza Dehghani, Markus Gödderz, Dominic Winter
The identification of large numbers of phosphopeptides from complex samples largely relies on sample fractionation to reduce complexity and allow using large amounts of starting material. For such experiments, commonly fractionation of whole cell lysate digests followed by enrichment of phosphopeptides from the single fractions is performed. We evaluated the tip-based fractionation of batch-enriched phosphopeptides as an alternative method. We compared three tip-based fractionation methods employing strong cation exchange (SCX), strong anion exchange (SAX), and C18 material for basic reversed-phase (BRP) fractionation using HeLa whole cell lysate digests...
November 10, 2017: Journal of Proteome Research
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