7,116 results match your criteria Journal of Proteome Research [Journal]


An Optimised Method for the Proteomic Analysis of Low Volumes of Cell Culture Media and the Secretome: The Application and the Demonstration of Altered Protein Expression in iPSC-Derived Neuronal Cell Lines from Parkinson's Disease Patients.

J Proteome Res 2018 Dec 18. Epub 2018 Dec 18.

Traditionally, cell culture medium in iPSC-derived cell work is not the main focus of research and often considered as just "food for cells". We demonstrate that by manipulation of the media and optimised methodology, it is possible to use this solution to study the proteins that the cell secretes ("secretome"). This is particularly useful in the study of iPSC-derived neurons, which require long culture time. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00831DOI Listing
December 2018

MetProc: separating measurement artifacts from true metabolites in an untargeted metabolomics experiment.

J Proteome Res 2018 Dec 18. Epub 2018 Dec 18.

High-throughput metabolomics using liquid chromatography and mass spectrometry (LC/MS) provide a useful method to identify biomarkers of disease and explore biological systems. However, the majority of metabolic features detected from untargeted metabolomics experiments have unknown ion signatures, making it critical that data should be thoroughly quality controlled to avoid analyzing false signals. Here we present a post-alignment method relying on intermittent pooled study samples to separate genuine metabolic features from potential measurement artifacts. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00893DOI Listing
December 2018

An averaging strategy to reduce variability in target-decoy estimates of false discovery rate.

J Proteome Res 2018 Dec 18. Epub 2018 Dec 18.

Decoy database search with target-decoy competition (TDC) provides an intuitive, easy-to-implement method for estimating the false discovery rate (FDR) associated with spectrum identifications from shotgun proteomics data. However, the procedure can yield different results for a fixed dataset analyzed with different decoy databases, and this decoy-induced variability is particularly problematic for smaller FDR thresholds, datasets or databases. The averaged TDC protocol combats this problem by exploiting multiple independently shuffled decoy databases to provide an FDR estimate with reduced variability. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00802DOI Listing
December 2018

Data-independent Acquisition for the Orbitrap Q Exactive HF. A tutorial.

J Proteome Res 2018 Dec 17. Epub 2018 Dec 17.

Data-independent acquisition (DIA) is a powerful mass spectrometric technique to perform both protein identification and quantification of complex protein samples. Setting up DIA methods on Orbitrap analyzers requires a thorough overview over the actions the Orbitrap mass spectrometers carry out. This tutorial is written with the intention to give an overview over the important parameters to consider as well as which measurements to carry out to get the most out of your DIA method when setting it up on an Orbitrap mass analyzer. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00845
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http://dx.doi.org/10.1021/acs.jproteome.8b00845DOI Listing
December 2018
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Label-free Proteomic Analysis of Exosomes Secreted from THP-1-derived Macrophages Treated with IFN-α Identifies Antiviral Proteins Enriched in Exosomes.

J Proteome Res 2018 Dec 14. Epub 2018 Dec 14.

Exosomes are extracellular vesicles that function in intercellular communication. We have previously reported that exosomes play an important role in the transmission of antiviral molecules during interferon-α (IFN-α) treatment. In this study, the protein profiles of THP-1-derived macrophages with or without interferon-α treatment and the exosomes secreted from these cells were analyzed by label-free LC-MS/MS quantitation technologies. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00514DOI Listing
December 2018

Isobaric Labeling Quantitative Metaproteomics for the Study of Gut Microbiome Response to Arsenic.

J Proteome Res 2018 Dec 14. Epub 2018 Dec 14.

Quantitative metaproteomics is a relatively new research field by applying proteomics technique to study microbial proteins of microbiome, and holds the great potential to truly quantify the functional proteins actually expressed by microbes in the biological environment such as gastrointestinal tract. The significant association between arsenic exposure and gut microbiome perturbations has been reported; however, metaproteomics has not yet been applied to study arsenic induced proteome changes of microbiome. Most importantly, to our knowledge, isobaric-labeling based large-scale metaproteomics has not been reported using the advanced database search approaches such as MetaPro-IQ and matched metagenome database search strategies to provide high quantification accuracy and less missing quantification values. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00666DOI Listing
December 2018

LC-MS-Based Metabolomics and Lipidomics Study of High-Density-Lipoprotein-Modulated Glucose Metabolism with an apoA-I Knockout Mouse Model.

J Proteome Res 2018 Dec 13. Epub 2018 Dec 13.

Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center for Life Sciences , Peking University Health Science Center , Beijing 100191 , China.

Type 2 diabetes mellitus (T2DM) has become a tremendous problem in public health nowadays. High-density lipoprotein (HDL) refers to a group of heterogeneous particles that circulate in blood, and a recent research finds that HDL acts a pivotal part of glucose metabolism. To understand systemic metabolic changes correlated with HDL in glucose metabolism, we applied LC-MS-based metabolomics and lipidomics to detect metabolomic and lipidomic profiles of plasma from apoA-I knockout mice fed a high-fat diet. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00290
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http://dx.doi.org/10.1021/acs.jproteome.8b00290DOI Listing
December 2018
1 Read

A tandem mass spectrometry sequence database search method for identification of O-fucosylated proteins by mass spectrometry.

J Proteome Res 2018 Dec 7. Epub 2018 Dec 7.

Thrombospondin type 1 repeats (TSRs), small adhesive protein domains with a wide range of functions, are usually modified with O-linked fucose, which may be extended to O-fucose-β1,3-glucose. Collision-induced dissociation (CID) spectra of O-fucosylated peptides cannot be sequenced by standard tandem mass spectrometry (MS/MS) sequence database search engines because O-linked glycans are highly labile in the gas phase and are effectively absent from the CID peptide fragment spectra, resulting in a large mass error. Electron transfer dissociation (ETD) preserves O-linked glycans on peptide fragments, but only a subset of tryptic peptides with low m/z can be reliably sequenced from ETD spectra compared to CID. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00638DOI Listing
December 2018

DeltaMass: Automated detection and visualization of mass shifts in proteomic open search results.

J Proteome Res 2018 Dec 7. Epub 2018 Dec 7.

Routine identification of thousands of proteins in a single LC/MS experiment has long become the norm. With these vast amounts of data more rigorous treatment of modified forms of peptides becomes possible. "open search" - a protein database search with a large precursor ion mass tolerance window, is becoming a popular method to evaluate possible sets of post-translational and chemical modifications in samples. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00728DOI Listing
December 2018

PPIP: An automated software for identification of bioactive endogenous peptides.

J Proteome Res 2018 Dec 12. Epub 2018 Dec 12.

Endogenous peptides play an important role in multiple biological processes in many species. Liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) is an important technique for detecting these peptides at a large scale. Herein, we present PPIP, which is a dedicated peptidogenomics software for identifying endogenous peptides based on peptidomics and RNA-Seq data. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00718
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http://dx.doi.org/10.1021/acs.jproteome.8b00718DOI Listing
December 2018
2 Reads

Scop3D: online visualization of mutation rates on protein structure.

J Proteome Res 2018 Dec 12. Epub 2018 Dec 12.

Scop3D is a tool that automatically annotates protein structure with sequence conservation starting from a set of protein sequence variants. Here, we present a complete upgrade and rewrite of Scop3D. We have included a DNA module that allows the analysis of single nucleotide polymorphisms in relation to the structural context of the protein. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00681DOI Listing
December 2018

Dasatinib is preferentially active in the activated B-cell subtype of diffuse large B-cell lymphoma.

J Proteome Res 2018 Dec 12. Epub 2018 Dec 12.

Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease, with at least one-third of its patients relapsing after treatment with the current chemotherapy regimen, R-CHOP. By gene expression profiling, patients with DLBCL can be categorized into two clinically relevant subtypes: activated B-cell (ABC) and germinal center B-cell (GCB) DLBCL. Patients with the ABC subtype have a poorer prognosis than those with GCB, and are defined by chronic, overactive signaling through the B-cell receptor and NF-κB pathways. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00841
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http://dx.doi.org/10.1021/acs.jproteome.8b00841DOI Listing
December 2018
2 Reads

The metabolic signature of Primary Biliary Cholangitis and its comparison with Coeliac Disease.

J Proteome Res 2018 Dec 12. Epub 2018 Dec 12.

Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease characterized by ongoing inflammatory destruction of the interlobular bile ducts, eventually leading to chronic cholestasis and biliary cirrhosis. This study primarily aims to define the metabolomic signature of PBC after comparison with healthy controls (HC). Secondly it aims at evaluating the possible metabolic association between PBC and coeliac disease (CD), an immune-mediated disorder frequently associated with PBC. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00849
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http://dx.doi.org/10.1021/acs.jproteome.8b00849DOI Listing
December 2018
2 Reads

Rapidly Assessing the Quality of Targeted Proteomics Experiments Through Monitoring Stable-isotope Labeled Standards.

J Proteome Res 2018 Dec 7. Epub 2018 Dec 7.

Targeted proteomics experiments based on selected reaction monitoring (SRM) have gained wide adoption in clinical biomarker, cellular modeling and numerous other biological experiments due to their highly accurate and reproducible quantification. The quantitative accuracy in targeted proteomics experiments is reliant on the stable-isotope, heavy-labeled peptide standards which are spiked into a sample and used as a reference when calculating the abundance of endogenous peptides. Therefore, the quality of measurement for these standards is a critical factor in determining whether data acquisition was successful. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00688DOI Listing
December 2018

ComPIL 2.0: An Updated Comprehensive Metaproteomics Database.

J Proteome Res 2018 Dec 10. Epub 2018 Dec 10.

We designed a metaproteomic analysis method (ComPIL) to accommodate the ever-increasing number of sequences against which experimental shotgun proteomics spectra could be accurately and rapidly queried. Our objective was to create these large databases for the analysis of complex meta-samples with unknown composition, including those derived from human, animal, and environmental microbiomes. The amount of high-throughput sequencing data has substantially increased since our original database was assembled in 2014. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00722DOI Listing
December 2018

PaDuA: a Python library for high-throughput (phospho)proteomic data analysis.

J Proteome Res 2018 Dec 10. Epub 2018 Dec 10.

The increased speed and sensitivity in mass spectrometry-based proteomics has encouraged its use in biomedical research in recent years. Large-scale detection of proteins in cells, tissues and whole organisms yields highly-complex quantitative data, the analysis of which poses significant challenges. Standardized proteomic workflows are necessary to ensure automated, sharable and reproducible proteomics analysis. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00576DOI Listing
December 2018

Proxl (Protein Cross-linking Database): A public server, QC tools, and other major updates.

J Proteome Res 2018 Dec 11. Epub 2018 Dec 11.

Proxl is an open source web application for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data and results. Proxl's core features include comparing datasets, structural analysis, customizable and interactive data visualizations, access to all underlying mass spectrometry data, and quality control tools. All features of Proxl are designed to be independent of specific cross-linker chemistry or software analysis pipelines. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00726DOI Listing
December 2018
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A Well-Controlled BioID Design for Endogenous Bait Proteins.

J Proteome Res 2018 Dec 10. Epub 2018 Dec 10.

VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.

The CRISPR/Cas9 revolution is profoundly changing the way life sciences technologies are used. Many assays now rely on engineered clonal cell lines to eliminate the overexpression of bait proteins. Control cell lines are typically nonengineered cells or engineered clones, implying a considerable risk for artifacts because of clonal variation. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00367DOI Listing
December 2018

Discovery and qualification of candidate urinary biomarkers of disease activity in lupus nephritis.

J Proteome Res 2018 Dec 10. Epub 2018 Dec 10.

Lupus nephritis (LN) is a severe clinical manifestation of systemic lupus erythematosus (SLE) associated with significant morbidity and mortality. Assessment of severity and activity of renal involvement in SLE requires a kidney biopsy, an invasive procedure with limited prognostic value. Non-invasive biomarkers are needed to inform treatment decisions and to monitor disease activity. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00874DOI Listing
December 2018

Tools for 3D Interactome Visualization.

J Proteome Res 2018 Dec 18. Epub 2018 Dec 18.

Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States.

In cells, intra- and intermolecular interactions of proteins confer function, and the dynamic modulation of this interactome is critical to meet the changing needs required to support life. Cross-linking and mass spectrometry (XL-MS) enable the detection of both intra- and intermolecular protein interactions in organelles, cells, tissues, and organs. Quantitative XL-MS enables the detection of interactome changes in cells due to environmental, phenotypic, pharmacological, or genetic perturbations. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00703
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http://dx.doi.org/10.1021/acs.jproteome.8b00703DOI Listing
December 2018
2 Reads

Characterization of the Blister Fluid Proteome for Pediatric Burn Classification.

J Proteome Res 2018 Dec 6. Epub 2018 Dec 6.

Blister fluid (BF) is a novel and viable research matrix for burn injury study, which can reflect both systemic and local micro-environmental responses. The protein abundance in BF from different burn severities were initially observed using a 2D SDS-PAGE approach. Subsequently, a quantitative data independent acquisition (DIA) method - SWATHTM was employed to characterize the proteome of pediatric burn blister fluid. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00355
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http://dx.doi.org/10.1021/acs.jproteome.8b00355DOI Listing
December 2018
4 Reads

Metabolic Signatures of Cystic Fibrosis Identified in Dried Blood Spots For Newborn Screening Without Carrier Identification.

J Proteome Res 2018 Dec 3. Epub 2018 Dec 3.

Cystic fibrosis (CF) is a complex multi-organ disorder that is among the most common fatal genetic diseases benefiting from therapeutic interventions early in life. Newborn screening (NBS) for pre-symptomatic detection of CF currently relies on a two-stage immunoreactive trypsinogen (IRT) and cystic fibrosis transmembrane conductance regulator (CFTR) mutation panel algorithm that is sensitive, but not specific for identifying affected neonates with a low positive predictive value. For the first time, we report the discovery of a panel of CF-specific metabolites from a single 3. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00351DOI Listing
December 2018
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TomahaqCompanion: A tool for the creation and analysis of isobaric label based multiplexed targeted assays.

J Proteome Res 2018 Dec 3. Epub 2018 Dec 3.

Triggered by Offset, Multiplexed, Accurate mass, High resolution, and Absolute Quantitation (TOMAHAQ) is a recently introduced targeted proteomics method that combines peptide and sample multiplexing. TOMAHAQ assays enable sensitive and accurate multiplexed quantification by implementing an intricate data collection scheme that comprises multiple MSn scans, mass inclusion lists, and data-driven filters. Consequently, manual creation of TOMAHAQ methods can be time consuming and error prone while the resulting TOMAHAQ data may not be compatible with common mass spectrometry analysis pipelines. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00767DOI Listing
December 2018

Vegetable signatures derived from human urinary metabolomic data in controlled feeding studies.

J Proteome Res 2018 Dec 5. Epub 2018 Dec 5.

Examination of changes in urinary metabolomic profiles after vegetable ingestion may lead to new methods of assessing plant food intake. To this regard, we developed a proof-of-principle methodology to identify urinary metabolomic signatures for spinach, celery, and onion. Three feeding studies were conducted. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00470DOI Listing
December 2018

RNA-binding proteomics reveals MATR3 interacting with lncRNA SNHG1 to enhance neuroblastoma progression.

J Proteome Res 2018 Dec 5. Epub 2018 Dec 5.

The interaction of long noncoding RNAs (lncRNAs) with one or more RNA-binding proteins (RBPs) are important to a plethora of cellular and physiological processes. The lncRNA SNHG1 was reported to be aberrantly expressed and associated with poor patient prognosis in several cancers, including neuroblastoma. However, the interacting RBPs and biological functions associated with SNHG1 in neuroblastoma remains unknown. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00693DOI Listing
December 2018
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An update on the moFF Algorithm for label-free quantitative proteomics.

J Proteome Res 2018 Dec 4. Epub 2018 Dec 4.

moFF is a modular and operating system independent tool for quantitative analysis of label-free mass-spectrometry based proteomics data. The moFF workflow, comprising matching-between-runs and apex quantification, can be applied to any upstream search engine's output, along with the corresponding Thermo or mzML raw file. We here present moFF 2. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00708
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http://dx.doi.org/10.1021/acs.jproteome.8b00708DOI Listing
December 2018
3 Reads

msCRUSH: fast tandem mass spectral clustering using locality sensitive hashing.

J Proteome Res 2018 Dec 4. Epub 2018 Dec 4.

Large-scale proteomics projects often generate massive and highly redundant tandem mass spectra(MS/MS). Spectral clustering algorithms can reduce the redundancy in these datasets, and thus speed up database searching for peptide identification, a major bottleneck for proteomic data analysis. The key challenge of spectral clustering is to reduce the redundancy in the MS/MS spectra data, while retaining sufficient sensitivity to identify peptides from the clustered spectra. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00448DOI Listing
December 2018

Proteomic Profiling of Human Hepatic Stellate Cell Line LX2 Responses to Irradiation and TGF-β1.

J Proteome Res 2018 Nov 29. Epub 2018 Nov 29.

Hepatic stellate cells (HSCs) are the main target of radiation damage and primarily contribute to the development of radiation-induced liver fibrosis. However, the molecular events underlying the radiation-induced activation of HSCs are not fully elucidated. In the present study, human HSC line LX2 was treated with X-ray irradiation and/or TGF-β1 and profibrogenic molecules were evaluated. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00814DOI Listing
November 2018
1 Read

Site-specific K63 ubiquitinomics provides insights into translation regulation under stress.

J Proteome Res 2018 Nov 29. Epub 2018 Nov 29.

During oxidative stress, K63-linked polyubiquitin chains accumulate in the cell and modify a variety of proteins including ribosomes. Knowledge of the precise sites of K63 ubiquitination is key to understand its function during the response to stress. To identify the sites of K63 ubiquitin, we developed a new mass-spectrometry based method that quantified >1,100 K63 ubiquitination sites in yeast responding to oxidative stress induced by H2O2. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00623DOI Listing
November 2018
2 Reads

Discovery and quantification of non-human proteins in human milk.

J Proteome Res 2018 Nov 29. Epub 2018 Nov 29.

The question whether and which non-human peptides or proteins are present in human milk was raised many decades ago. However, due to cross-reactivity or nonspecific antibody recognition, the accuracy of detection by immunochemical methods has been a concern. Additionally, the relative low-abundance of non-human peptides/proteins in the complex milk sample makes them a challenging target to detect. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00550DOI Listing
November 2018

Large-Scale Longitudinal Metabolomics Study Reveals Different Trimester-specific Alterations of Metabolites in Relation to Gestational Diabetes Mellitus.

J Proteome Res 2018 Nov 29. Epub 2018 Nov 29.

Despite the increasing research attention paid to gestational diabetes mellitus (GDM) due to its high prevalence, limited knowledge is available about its pathogenesis. In this study, 428 serum samples were collected from 107 pregnant women suffering GDM and 107 matched healthy controls. The non-targeted metabolomics data of maternal serum samples from the first (T1, n = 214) and second trimesters (T2, n = 214) were acquired by using ultra-high performance liquid chromatography coupled with Orbitrap mass spectrometry (MS). Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00602DOI Listing
November 2018
3 Reads

Ultraviolet Photodissociation of ESI and MALDI generated protein ions on a Q-Exactive mass spectrometer.

J Proteome Res 2018 Nov 28. Epub 2018 Nov 28.

The identification of molecular ions produced by MALDI or ESI strongly relies on their fragmentation to structurally informative fragments. The widely diffused fragmentation techniques for ESI multiply charged ions, are either incompatible (ECD and ETD) or show lower efficiency (CID, HCD), with the predominantly singly charged peptide and protein ions formed by MALDI. In source decay (ISD) has been successfully adopted to sequence MALDI generated ions, but it further increases spectral complexity and it is not compatible with Mass Spectrometry Imaging. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00896DOI Listing
November 2018

Hippocampal proteomic alteration in triple transgenic mouse model of Alzheimer's disease and implication of PINK 1 regulation in donepezil treatment.

J Proteome Res 2018 Nov 28. Epub 2018 Nov 28.

Background: Donepezil is a clinically approved acetylcholinesterase inhibitor (AChEI) for cognitive improvement in Alzheimer's disease (AD). Donepezil has been used as a first-line therapeutics for the symptomatic treatment of AD, but its ability to modify disease pathology and underlying mechanisms are not clear.

Methods: We investigated the protective effects and underlying mechanisms of donepezil in AD-related triple transgenic (APPSwe/PSEN1M146V/MAPTP301L) mouse model (3×Tg-AD). Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00818DOI Listing
November 2018

Data-independent acquisition mass spectrometry to quantify protein levels in FFPE tumor biopsies for molecular diagnostics.

J Proteome Res 2018 Nov 27. Epub 2018 Nov 27.

Mass spectrometry-based protein quantitation is currently used to measure therapeutically relevant protein biomarkers in CAP/CLIA setting to predict likely responses of known therapies. Selected reaction monitoring (SRM) is the method of choice due to its outstanding analytical performance. However, data-independent acquisition (DIA) is now emerging as a proteome-scale clinical assay. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00699
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http://dx.doi.org/10.1021/acs.jproteome.8b00699DOI Listing
November 2018
2 Reads

TKO6: A Peptide Standard to Assess Interference for Unit-Resolved Isobaric Labeling Platforms.

J Proteome Res 2018 Nov 27. Epub 2018 Nov 27.

Protein abundance profiling using isobaric labeling is a well-established quantitative mass spectrometry technique. However, ratio distortion resulting from co-isolated and co-fragmented ions - commonly referred to as interference - remains a drawback of this technique. Tribrid mass spectrometers, such as the Orbitrap Fusion and the Orbitrap Fusion Lumos with a triple mass analyzer configuration, facilitate methods (namely SPS-MS3) that can help alleviate interference. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00902
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http://dx.doi.org/10.1021/acs.jproteome.8b00902DOI Listing
November 2018
2 Reads

Unique diversity of sting-related toxins based on transcriptomic and proteomic analysis of the jellyfish Cyanea capillata and Nemopilema nomurai (Cnidaria: Scyphozoa).

J Proteome Res 2018 Nov 27. Epub 2018 Nov 27.

The scyphozoan jellyfish Cyanea capillata and Nemopilema nomurai are common blooming species in China. They possess heterogeneous nematocysts and produce various types of venom that can elicit diverse sting symptoms in humans. However, the differences in venom composition between the two species remain unclear. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00735DOI Listing
November 2018
1 Read

200+ Protein Concentrations in Healthy Human Blood Plasma: Targeted Quantitative SRM SIS Screening of Chromosomes 18, 13, Y and the Mitochondrial Chromosome Encoded Proteome.

J Proteome Res 2018 Nov 27. Epub 2018 Nov 27.

This work continues the series of the quantitative measurements of the proteins encoded by different chromosomes in the blood plasma of a healthy person. Selected Reaction Monitoring with Stable Isotope-labeled peptide Standards (SRM SIS) and a gene-centric approach, which is the basis for the implementation of the international Chromosome-centric Human Proteome Project (C-HPP), were applied for the quantitative measurement of proteins in human blood plasma. Analyses were carried out in the frame of C-HPP for each protein-coding gene of the four human chromosomes: 18, 13, Y and mitochondrial. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00391DOI Listing
November 2018

Colonic Proteome Signature in Immunoproteasome-Deficient Stressed Mice and Its Relevance for Irritable Bowel Syndrome.

J Proteome Res 2018 Nov 26. Epub 2018 Nov 26.

INSERM unit 1073 , Normandie University, UNIROUEN , 22 boulevard Gambetta , Rouen , F-76183 , France.

A role for immunoproteasome in the regulation of intestinal permeability has been previously suggested both in mice during water avoidance stress (WAS) and in patients with irritable bowel syndrome (IBS). Here, we provide evidence that the ubiquitin-proteasome system (UPS) contributes to the pathophysiology of IBS. Indeed, we report that colonic proteome is altered in WAS mice and that β2i subunit deficiency modifies the proteome response that is associated with a limitation of colonic hyperpermeability. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00793DOI Listing
November 2018

Protein inference using PIA workflows and PSI standard file formats.

J Proteome Res 2018 Nov 26. Epub 2018 Nov 26.

Proteomics using LC-MS/MS has become one of the main methods to analyze the proteins in biological samples in high-throughput. But the existing mass spectrometry instruments are still limited with respect to resolution and measurable mass ranges, which is one of the main reasons why shotgun proteomics is the major approach. Here, proteins are digested, which leads to the identification and quantification of peptides instead. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00723
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http://dx.doi.org/10.1021/acs.jproteome.8b00723DOI Listing
November 2018
4 Reads

Unipept 4.0: functional analysis of metaproteome data.

J Proteome Res 2018 Nov 22. Epub 2018 Nov 22.

Unipept (https://unipept.ugent.be) is a web application for metaproteome data analysis, with an initial focus on tryptic peptide based biodiversity analysis of MS/MS samples. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00716DOI Listing
November 2018

ASSESSING AUTOMATED SAMPLE PREPARATION TECHNOLOGIES FOR HIGH-THROUGHPUT PROTEOMICS OF FROZEN WELL CHARACTERIZED TISSUES FROM SWEDISH BIOBANKS.

J Proteome Res 2018 Nov 21. Epub 2018 Nov 21.

Large cohorts of carefully collected clinical tissue materials play a central role in acquiring sufficient depth and statistical power to discover disease-related mechanisms and biomarkers of clinical significance. Manual preparation of such large sample cohorts requires experienced laboratory personnel. This carries other possible downsides such as low throughput, high risk of errors and low reproducibility. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00792DOI Listing
November 2018
1 Read

RawTools: Rapid and Dynamic Interrogation of Orbitrap Data Files for Mass Spectrometer System Management.

J Proteome Res 2018 Nov 21. Epub 2018 Nov 21.

Optimizing the quality of proteomics data collected from a mass spectrometer (MS) requires careful selection of acquisition parameters and proper assessment of instrument performance. Software tools capable of extracting a broad set of information from raw files, including meta, scan, quantification, and identification data are needed to provide guidance for MS system management. In this work, direct extraction and utilization of these data is demonstrated using RawTools, a standalone tool for extracting meta and scan data directly from raw MS files generated on Thermo Orbitrap instruments. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00721DOI Listing
November 2018
1 Read

Web-Based Search Tool for Visualizing Instrument Performance Using the Triple Knockout (TKO) Proteome Standard.

J Proteome Res 2018 Nov 27. Epub 2018 Nov 27.

Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States.

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 coisolated and cofragmented 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. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00737DOI Listing
November 2018

MSstatsQC 2.0: R/Bioconductor package for statistical quality control of mass spectrometry-based proteomic experiments.

J Proteome Res 2018 Nov 19. Epub 2018 Nov 19.

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. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00732DOI Listing
November 2018

Cytoscape stringApp: Network analysis and visualization of proteomics data.

J Proteome Res 2018 Nov 19. Epub 2018 Nov 19.

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. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00702DOI Listing
November 2018

Accelerated Barocycler Lysis and Extraction Sample Preparation for Clinical Proteomics by Mass Spectrometry.

J Proteome Res 2018 Nov 28. Epub 2018 Nov 28.

ProCan, Children's Medical Research Institute, Faculty of Medicine and Health , University of Sydney , Westmead , NSW 2145 , Australia.

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 solubilization and reliable, controlled proteolytic digestion. Here, a previously reported PCT based protocol was optimized using 1-4 mg biopsy punches from rat kidney. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00684DOI Listing
November 2018
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Response to "Determining Allele-Specific Protein Expression (ASPE) Using a Novel Quantitative Concatamer Based Proteomics Method".

J Proteome Res 2018 Nov 20. Epub 2018 Nov 20.

Centre for Applied Pharmacokinetic Research , University of Manchester , Stopford Building, Oxford Road , Manchester M13 9PT , U.K.

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, 17 (10), 3606-3612, DOI: 10. Read More

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http://dx.doi.org/10.1021/acs.jproteome.8b00871DOI Listing
November 2018

Complementary iTRAQ Proteomic and Transcriptomic Analyses of Leaves in Tea Plant ( Camellia sinensis L.) with Different Maturity and Regulatory Network of Flavonoid Biosynthesis.

J Proteome Res 2018 Nov 26. Epub 2018 Nov 26.

Tea Research Institute , Zhejiang University , Hangzhou 310013 , China.

The quality of tea is highly related with the maturity of the fresh tea leaves 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. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00578
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http://dx.doi.org/10.1021/acs.jproteome.8b00578DOI Listing
November 2018
10 Reads

EBprotV2: A Perseus Plugin for Differential Protein Abundance Analysis of Labeling-Based Quantitative Proteomics Data.

J Proteome Res 2018 Nov 19. Epub 2018 Nov 19.

Department of Medicine, Yong Loo Lin School of Medicine , National University of Singapore , Singapore 117599 , Singapore.

We present EBprotV2, a Perseus plugin for peptide-ratio-based differential protein abundance 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 abundant proteins and nondifferentially abundant proteins and computes the probability score of differential abundance 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 data sets containing a large number of peptides (e. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00483
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http://dx.doi.org/10.1021/acs.jproteome.8b00483DOI Listing
November 2018
5 Reads
4.250 Impact Factor

Multiplex Assay for Quantification of Acute Phase Proteins and Immunoglobulin A in Dried Blood Spots.

J Proteome Res 2018 Nov 20. Epub 2018 Nov 20.

Research Centre for Toxic Compounds in the Environment , Masaryk University , Brno , Czech Republic.

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. Read More

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http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00657
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http://dx.doi.org/10.1021/acs.jproteome.8b00657DOI Listing
November 2018
2 Reads