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Journal of Proteome Research

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https://www.readbyqxmd.com/read/30451507/a-web-based-search-tool-for-visualizing-instrument-performance-using-the-triple-knockout-tko-proteome-standard
#1
Jeremy P Gygi, Qing Yu, Jose Navarrete-Perea, Ramin Rad, Steven P Gygi, Joao A Paulo
Multiplexing strategies are at the forefront of mass spectrometry-based proteomics, with SPS-MS3 methods becoming increasingly commonplace. A known caveat of isobaric multiplexing is interference resulting from co-isolated and co-fragmented ions that do not originate from the selected precursor of interest. The triple knockout (TKO) standard was designed to benchmark data collection strategies to minimize interference. However, a limitation to its widespread use has been the lack of an automated analysis platform...
November 19, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30450913/msstatsqc-2-0-r-bioconductor-package-for-statistical-quality-control-of-mass-spectrometry-based-proteomic-experiments
#2
Eralp Dogu, Sara Mohammad Taheri, Roger Olivella, Florian Marty, Ian Lienert, Lukas Reiter, Eduardo Sabidó, Olga Vitek
MSstatsQC is an R/Bioconductor package for statistical monitoring of longitudinal system suitability and quality control in mass spectrometry-based proteomics. MSstatsQC was initially designed for targeted Selected Reaction Monitoring experiments. This manuscript presents an extension, MSstatsQC 2.0, that supports experiments with global Data-Dependent and Data-Independent acquisition. The extension implements data processing and analyses that are specific to these acquisition types. It relies on the state-of-the-art methods of statistical process control to detect deviations from optimal performance of various metrics (such as intensity and retention time of chromatographic peaks), and to summarize the results across multiple metrics and analytes...
November 19, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30450911/cytoscape-stringapp-network-analysis-and-visualization-of-proteomics-data
#3
Nadezhda T Doncheva, John Morris, Jan Gorodkin, Lars J Jensen
Protein networks have become a popular tool for analyzing and visualizing the often long lists of proteins or genes obtained from proteomics and other high-throughput technologies. One of the most popular sources of such networks is the STRING database, which provides protein networks for more than 2000 organisms, including both physical interactions from experimental data and functional associations from curated pathways, automatic text mining, and prediction methods. However, its web interface is mainly intended for inspection of small networks and their underlying evidence...
November 19, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30407017/extended-sialylated-o-glycan-repertoire-of-human-urinary-glycoproteins-discovered-and-characterized-using-electron-transfer-higher-energy-collision-dissociation
#4
Zsuzsanna Darula, Ádám Pap, Katalin F Medzihradszky
A relatively novel activation technique, electron-transfer/higher-energy collision dissociation (EThcD) was used in the LC-MS/MS analysis of tryptic glycopeptides enriched with wheat germ agglutinin from human urine samples. We focused on the characterization of mucin-type O-glycopeptides. EThcD in a single spectrum provided information on both the peptide modified and the glycan carried. Unexpectedly, glycan oxonium ions indicated the presence of O-acetyl, and even O-diacetyl-sialic acids. B and Y fragment ions revealed that (i) in core 1 structures the Gal residue featured the O-acetyl-sialic acid, when there was only one in the glycan; (ii) several glycopeptides featured core 1 glycans with disialic acids, in certain instances O-acetylated; (iii) the disialic acid was linked to the GalNAc residue whatever the degree of O-acetylation; (iv) core 2 isomers with a single O-acetyl-sialic acid were chromatographically resolved...
November 19, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30394098/large-scale-modeling-approach-reveals-functional-metabolic-shifts-during-hepatic-differentiation
#5
Nathalie Poupin, Anne Corlu, Nicolas J Cabaton, Hélène Dubois-Pot-Schneider, Cécile Canlet, Elodie Person, Sandrine Bruel, Clément Frainay, Florence Vinson, Florence Maurier, Fabrice Morel, Marie-Anne Robin, Bernard Fromenty, Daniel Zalko, Fabien Jourdan
Being able to explore the metabolism of broad metabolizing cells is of critical importance in many research fields. This article presents an original modeling solution combining metabolic network and omics data to identify modulated metabolic pathways and changes in metabolic functions occurring during differentiation of a human hepatic cell line (HepaRG). Our results confirm the activation of hepato-specific functionalities and newly evidence modulation of other metabolic pathways, which could not be evidenced from transcriptomic data alone...
November 19, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30351951/targeted-ubiquitin-proteasomal-proteolysis-pathway-in-chronic-social-defeat-stress
#6
Hsiao-Yun Lin, Yu-Shu Liu, Yu-Ching Liu, Chao-Jung Chen, Dah-Yuu Lu
Stressful events promote psychopathogenic changes that might contribute to the development of mental illnesses. Some individuals tend to recover from the stress response, while some do not. However, the molecular mechanisms of stress resilience during stress are not well-characterized. Here, we identify proteomic changes in the hippocampus using proteomic technique to examine mice following chronic social defeat stress. We showed that small ubiquitin-like modifier (SUMO)-1 expression was significantly decreased in susceptible mice following chronic social defeat stress...
November 19, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30444966/accelerated-barocycler-lysis-and-extraction-able-sample-preparation-for-clinical-proteomics-by-mass-spectrometry
#7
Natasha Lucas, Andrew B Robinson, Maiken Marcker Espersen, Sadia Mahboob, Dylan Xavier, Jing Xue, Rosemary L Balleine, Anna deFazio, Peter G Hains, Phillip J Robinson
We have developed a streamlined proteomic sample preparation protocol termed Accelerated Barocycler Lysis and Extraction (ABLE), that substantially reduces the time and cost of tissue sample processing. ABLE is based on pressure cycling technology (PCT) for rapid tissue solubilisation and reliable, controlled proteolytic digestion. Here, a previously reported PCT based protocol was optimised using 1-4 mg biopsy punches from rat kidney. The tissue denaturant urea was substituted with a combination of sodium deoxycholate (SDC) and N-propanol...
November 16, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30444614/response-to-determining-allele-specific-protein-expression-aspe-using-a-novel-quantitative-concatamer-based-proteomics-method
#8
Brahim Achour, Amin Rostami-Hodjegan, Jill Barber
A recent publication in this journal reported the application of a targeted proteomic strategy using a quantitative concatemer (QconCAT) standard to the assessment of allele-specific expression of UGT2B15 claiming this methodology to be a "novel" approach (J. Proteome Res. 2018, Doi: acs.jproteome.8b00620). While the application is not common, the method has previously been described and reported by our group, in relation to the quantification of CYP2B6 alleles, (J. Proteome Res. 2013, 12, 5934-42) to assess the expression of a prevalent polymorphism in a Caucasian population...
November 16, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30427694/complementary-itraq-proteomic-and-transcriptomic-analyses-of-leaves-in-tea-plant-camellia-sinensis-l-with-different-maturity-and-regulatory-network-of-flavonoid-biosynthesis
#9
Liang-Yu Wu, Zhou-Tao Fang, Jin-Ke Lin, Yun Sun, Zhi-Zheng Du, Ya-Ling Guo, Jiang-Hong Liu, Yue-Rong Liang, Jian-Hui Ye
The quality of tea is highly related with the maturity of fresh tea leaf at harvest. The present study investigated the proteomic and transcriptomic profiles of tea leaves with different maturity, using iTRAQ and RNA-seq technologies. A total of 4455 proteins and 27,930 unigenes were identified, with functional enrichment analyses of GO categorization and KEGG annotation. The compositions of flavonoids (catechins and flavonols) in tea leaves were determined. The total content of flavonoids decreased with leaf maturity, in accordance with the protein regulation patterns of shikimate, phenylpropanoid and flavonoid pathways...
November 14, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30394753/proteogenomic-analyses-of-cellular-lysates-using-a-phenol-guanidinium-thiocyanate-reagent
#10
Yusuke Kawashima, Jun Miyata, Takashi Watanabe, Juri Shioya, Makoto Arita, Osamu Ohara
Protein and RNA profiles are highly informative when generating a comprehensive understanding of the dynamics of complex biological systems. Quantitative correlations between protein and RNA profiles are not always high, yet simultaneous acquisition of both profiles remains challenging, in part because of the limited availability of samples and the inconvenience of separately preparing protein and RNA fractions. In a previous study, protein, DNA, and RNA fractions were simultaneously prepared from the same sample using phenol-guanidinium isothiocyanate reagent (P/GTC), although the performance of P/GTC-extracts in proteogenomic analyses remains poorly understood...
November 12, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30387359/insights-into-the-effects-of-crack-abuse-on-the-human-metabolome-using-a-nmr-approach
#11
Tássia B B C Costa, Acioly L T Lacerda, Caroline Dal Mas, Elisa Brietzke, João G M Pontes, Lucas A N Marins, Lucas G Martins, Marcel V Nunes, Mariana Pedrini, Michelle S C Carvalho, Milan P Mitrovitch, Mirian A F Hayashi, Natália L Saldanha, Ronei J Poppi, Ljubica Tasic
Approximately 255 million people consume illicit drugs every year, among which 18 million use cocaine. A portion of this drug is represented by crack, but it is difficult to estimate the number of users since most are marginalized. However, there are no recognized efficacious pharmacotherapies for crack-cocaine dependence. Inflammation and infection in cocaine users may be due to behavior adopted in conjunction with drug-related changes in the brain. To understand the metabolic changes associated with the drug abuse disorder and identify biomarkers, we performed a 1 H NMR-based metabonomic analysis of 44 crack users' and 44 healthy volunteers' blood serum...
November 12, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30411623/ebprotv2-a-perseus-plugin-for-differential-protein-abundance-analysis-of-labeling-based-quantitative-proteomics-data
#12
Hiromi W L Koh, Yunbin Zhang, Christine Vogel, Hyungwon Choi
We present EBprotV2, a Perseus plug-in for peptide ratio-based differential protein expression analysis in labeling-based proteomics experiments. The original version of EBprot models the distribution of log-transformed peptide-level ratios as a Gaussian mixture of differentially expressed proteins and non-differentially expressed proteins and computes the probability score of differential expression for each protein based on the reproducible magnitude of peptide ratios. However, the fully parametric model can be inflexible and its R implementation is time consuming for datasets containing a large number of peptides (e...
November 9, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30394750/distinguishing-between-spectral-clustering-and-cluster-analysis-of-mass-spectra
#13
Hélène Borges, Romain Guibert, Olga Permiakova, Thomas Burger
The term "spectral clustering" is sometimes used to refer to the clustering of mass spectrometry data. However, it also classically refers to a family of popular clustering algorithms. To avoid confusion, a more specific term could advantageously be coined.
November 9, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30408962/multiplex-assay-for-quantification-of-acute-phase-proteins-and-immunoglobulin-a-in-dried-blood-spots
#14
Veronika Vidova, Eliska Stuchlikova, Marketa Vrbova, Martina Almasi, Jana Klánová, Vojtech Thon, Zdenek Spacil
Inflammation is the first line defense mechanism against infection, tissue damage or cancer development. However, inappropriate inflammatory response may also trigger diseases. The quantification of inflammatory proteins is essential to distinguish between harmful and beneficial immune response. Currently used immunoanalytical assays may suffer specificity issues due to antigen-antibody interaction and possible cross-reactivity of antibody with other protein species. In addition, immunoanalytical assays typically require invasive blood sampling and additional logistics; they are relatively costly and highly challenging to multiplex...
November 8, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30406665/loss-of-setd2-induces-a-metabolic-switch-in-renal-cell-carcinoma-cell-lines-toward-enhanced-oxidative-phosphorylation
#15
Jingping Liu, Paul D Hanavan, Katon Kras, Yvette W Ruiz, Erik P Castle, Douglas F Lake, Xianfeng Chen, Daniel O'Brien, Huijun Luo, Keith D Robertson, Haiwei Gu, Thai H Ho
SETD2, a histone H3 lysine trimethyltransferase, is frequently inactivated and associated with recurrence of clear cell renal cell carcinoma (ccRCC). However, the impact of SETD2 loss on metabolic alterations in ccRCC is still unclear. In this study, SETD2 null isogenic 38E/38F clones derived from 786-O cells were generated by zinc finger nucleases, and subsequent metabolic, genomic, and cellular phenotypic changes were analyzed by targeted metabolomics, RNA-sequencing, and biological methods, respectively...
November 8, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30404448/single-amino-acid-variant-discovery-in-small-numbers-of-cells
#16
Zhijing Tan, Xinpei Yi, Nicholas J Carruthers, Paul M Stemmer, David M Lubman
We have performed deep proteomic profiling down to as few as 9 Panc-1 cells using sample fractionation, TMT multiplexing and a carrier/reference strategy. Off line fractionation of the TMT-labeled sample pooled with TMT-labeled carrier Panc-1 whole cell proteome was achieved using alkaline reversed phase spin columns. The fractionation in conjunction with the carrier/reference (C/R) proteome allowed us to detect 47,414 unique peptides derived from 6,261 proteins which provided a sufficient coverage to search for single amino acid variants (SAAVs) related to cancer...
November 7, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30394759/a-peptide-level-fully-annotated-dataset-for-quantitative-evaluation-of-precursor-aware-mass-spectrometry-data-processing-algorithms
#17
Jessica Henning, Annika Tostengard, Rob Smith
Modern label-free quantitative mass spectrometry workflows are complex experimental chains for devising the composition of biological samples. With benchtop and in silico experimental steps that each have a significant effect on the accuracy, coverage, and statistical significance of the study result, it is crucial to understand the efficacy and biases of each protocol decision. While many studies have been conducted on wet lab experimental protocols, post-acquisition data processing methods have not been adequately evaluated, in large part due to a lack of available ground truth data...
November 5, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30394099/multi-parameter-optimization-of-two-common-proteomics-quantification-methods-for-quantifying-low-abundance-proteins
#18
Chengqian Zhang, Zhaomei Shi, Ying Han, Yan Ren, Piliang Hao
Quantitative proteomics has been extensively applied in the screening of differentially regulated proteins in various research areas for decades, but its sensitivity and accuracy have been a bottleneck for many applications. Every step in the proteomics workflow can potentially affect the quantification of low-abundance proteins, but a systematic evaluation of their effects has not been done yet. In this work, to improve the sensitivity and accuracy of label-free quantification and tandem mass tags (TMT) labeling in quantifying low-abundance proteins, multi-parameter optimization was carried out using a complex 2-proteome artificial sample mixture for a series of steps from sample preparation to data analysis, including the desalting of peptides, peptide injection amount for LC-MS/MS, MS1 resolution, the length of LC-MS/MS gradient, AGC targets, ion accumulation time, MS2 resolution, precursor co-isolation threshold, data analysis software, statistical calculation methods and protein fold changes, and the best settings for each parameter were defined...
November 5, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30387612/global-ion-suppression-limits-the-potential-of-mass-spectrometry-based-phosphoproteomics
#19
Roland Felix Dreier, Erik Ahrné, Petr Broz, Alexander Schmidt
Mass spectrometry-based proteomics has become the method of choice to pinpoint and monitor thousands of post-translational modifications, predominately phosphorylation sites, in cellular signaling studies. Critical for achieving this analytical depth is the enrichment for phosphorylated peptides prior to LC-MS analysis. Despite the high prevalence of this modification, the numbers of identified phosphopeptides lag behind those achieved for unmodified peptides, and the cause for this still remains controversial...
November 2, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/30362351/flow-cytometry-has-a-significant-impact-on-the-cellular-metabolome
#20
Aleksandra Binek, David Rojo, Joanna Godzien, Francisco Javier Rupérez, Vanessa Nuñez, Inmaculada Jorge, Mercedes Ricote, Jesús Vázquez, Coral Barbas
The characterization of specialized cell subpopulations in a heterogeneous tissue is essential for understanding organ function in health and disease. A popular method of cell isolation is fluorescence-activated cell sorting (FACS) based on probes that bind surface or intracellular markers. In this study, we analyze the impact of FACS on the cell metabolome of mouse peritoneal macrophages. Compared with directly pelleted macrophages, FACS-treated cells had an altered content of metabolites related to the plasma membrane, activating a mechanosensory signaling cascade causing inflammation-like stress...
November 2, 2018: Journal of Proteome Research
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