Abstract：
:Workflows for large-scale (MS)-based shotgun proteomics can potentially lead to costly errors in the form of incorrect peptide-spectrum matches (PSMs). To improve the robustness of these workflows, we have investigated the use of the precursor mass discrepancy (PMD) to detect and filter potentially false PSMs that have, nonetheless, a high confidence score. We identified and addressed three cases of unexpected bias in PMD results: time of acquisition within a liquid chromatography-mass spectrometry (LC-MS) run, decoy PSMs, and length of the peptide. We created a postanalysis Bayesian confidence measure based on score and PMD, called PMD-false discovery rate (FDR). We tested PMD-FDR on four data sets across three types of MS-based proteomics projects: standard (single organism; reference database), proteogenomics (single organism; customized genomic-based database plus reference), and metaproteomics (microorganism community; customized conglomerate database). On a ground-truth data set and other representative data, PMD-FDR was able to detect 60-80% of likely incorrect PSMs (false-hits) while losing only 5% of correct PSMs (true-hits). PMD-FDR can also be used to evaluate data quality for results generated within different experimental PSM-generating workflows, assisting in method development. Going forward, PMD-FDR should provide detection of high scoring but likely false-hits, aiding applications that rely heavily on accurate PSMs, such as proteogenomics and metaproteomics.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Hubler SL,Kumar P,Mehta S,Easterly C,Johnson JE,Jagtap PD,Griffin TJdoi
10.1021/acs.jproteome.9b00478subject
Has Abstractpub_date
2020-01-03 00:00:00pages
161-173issue
1eissn
1535-3893issn
1535-3907journal_volume
19pub_type
杂志文章abstract：:Protein tyrosine nitration by oxidative and nitrate stress is important in the pathogenesis of many inflammatory or aging-related diseases. Mass spectrometry analysis of protein nitrotyrosine is very challenging because the non-nitrated peptides suppress the signals of the low-abundance nitrotyrosine (NT) peptides. No...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00275
更新日期：2017-08-04 00:00:00
abstract：:Robust quantification is an essential component of comparative -omic strategies. In this regard, glycomics lags behind proteomics. Although various isotope-tagging and direct quantification methods have recently enhanced comparative glycan analysis, a cell culture labeling strategy, that could provide for glycomics th...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr8010028
更新日期：2009-08-01 00:00:00
abstract：:Spectral library searching is a popular approach for MS/MS-based peptide identification. Because the size of spectral libraries continues to grow, the performance of searching algorithms is an important issue. This technical note introduces a strategy based on a minimum shared peak count between two spectra to reduce ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr401269z
更新日期：2014-09-05 00:00:00
abstract：:Metabolomic approaches have the potential to make an exceptional contribution to understanding how chemicals and other environmental stressors can affect both human and environmental health. However, the application of metabolomics to environmental exposures, although getting underway, has not yet been extensively exp...
journal_title：Journal of proteome research
pub_type： 杂志文章,评审
doi：10.1021/pr060623x
更新日期：2007-02-01 00:00:00
abstract：:This paper describes a metabonomic study of prenatal disorders using nuclear magnetic resonance (NMR) spectroscopy of amniotic fluid (AF) collected in the second trimester of pregnancy, to search for metabolite markers of fetal malformations, prediagnostic gestational diabetes (GD), preterm delivery (PTD), early ruptu...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100815q
更新日期：2010-11-05 00:00:00
abstract：:Vascular leakage is a hallmark of severe dengue infection. Although extensive studies have been conducted during the past several decades, the molecular mechanisms underlying vascular leakage in dengue shock syndrome (DSS) remain unclear. We thus performed a proteomics study to characterize responses in human endothel...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900060g
更新日期：2009-05-01 00:00:00
abstract：:Reference materials are vital to benchmarking the reproducibility of clinical tests and essential for monitoring laboratory performance for clinical proteomics. The reference material utilized for mass spectrometric analysis of the human proteome would ideally contain enough proteins to be suitably representative of t...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00165
更新日期：2018-06-01 00:00:00
abstract：:Ureteral obstruction will lead clinically to hydronephrosis, which may further develop into partial or complete loss of kidney function and even cause permanent histological damage. However, there is little knowledge of metabolic responses during the obstructed process and its recoverability. In this study, a complete...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00304
更新日期：2018-09-07 00:00:00
abstract：:Knowledge of protein subcellular localization assists in the elucidation of protein function and understanding of different biological mechanisms that occur at discrete subcellular niches. Organelle-centric proteomics enables localization of thousands of proteins simultaneously. Although such techniques have successfu...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4008464
更新日期：2014-02-07 00:00:00
abstract：:In-depth, reproducible coverage of complex proteomes is challenging because the complexity of tryptic digests subjected to LC-MS/MS analysis frequently exceeds mass spectrometer analytical capacity, which results in undersampling of data. In this study, we used cancer cell lysates to systematically compare the commonl...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900927y
更新日期：2010-02-05 00:00:00
abstract：:The SEQUEST program was the first and remains one of the most widely used tools for assigning a peptide sequence within a database to a tandem mass spectrum. The cross correlation score is the primary score function implemented within SEQUEST and it is this score that makes the tool particularly sensitive. Unfortunate...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800420s
更新日期：2008-10-01 00:00:00
abstract：:Crohn's disease is an inflammatory disorder of the bowel, believed to arise from the dysregulation of intestinal mucosal immunity. The interleukin-10-deficient (IL10-/-) mouse, which develops intestinal inflammation in the presence of gut microflora, serves as a mouse model of Crohn's disease. Nontargeted urinary meta...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800999t
更新日期：2009-04-01 00:00:00
abstract：:Butyrate, a fermentation product of the large bowel microflora, is potentially protective against the development of colorectal cancer. In vitro, butyrate has been shown to induce apoptosis and inhibit proliferation in numerous cancer cell lines, including colorectal cancer. Although these tumor suppressing properties...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr8009929
更新日期：2009-03-01 00:00:00
abstract：:Prediction of the types of membrane proteins is of great importance both for genome-wide annotation and for experimental researchers to understand proteins' functions. We describe a new strategy for the prediction of the types of membrane proteins using the Nearest Neighbor Algorithm. We introduced a bipartite feature...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr700715c
更新日期：2008-03-01 00:00:00
abstract：:Label-free quantification of shotgun proteomics data is a frequently used strategy, offering high dynamic range, sensitivity, and the ability to compare a high number of samples without additional labeling effort. Here, we present a bioinformatics approach that significantly improves label-free quantification results....
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00113
更新日期：2019-01-04 00:00:00
abstract：:Gram-negative and -positive bacteria elicit different response patterns by the host. The proteomic profiles of milk whey samples from cows naturally infected with Escherichia coli or Staphyloccocus aureus as compared to whey from healthy cows were determined by one-dimensional, liquid chromatography-tandem mass spectr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100336e
更新日期：2010-09-03 00:00:00
abstract：:MHC molecules present protein-derived peptides to T lymphocytes. By developing TiO2-based microcentrifugation columns, we identified the first phosphorylated MHC class I ligands from tumor tissue (renal cell carcinoma) and, by comparison to healthy renal tissue, found one Brf1-derived ligand as potentially tumor-assoc...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800937k
更新日期：2009-07-01 00:00:00
abstract：:We performed systematic evaluation of 38 protocols to concentrate normal human urinary proteins prior to 2D-PAGE analysis. Recovery yield and pattern of resolved protein spots were compared among different methods and intra-/inter-individual variabilities were examined. Precipitation with 90% ethanol provided the grea...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0502525
更新日期：2006-01-01 00:00:00
abstract：:HER2-testing in breast and gastric cancers is mandatory for the treatment with trastuzumab. We hypothesized that imaging mass spectrometry (IMS) of breast cancers may be useful for generating a classifier that may determine HER2-status in other cancer entities irrespective of primary tumor site. A total of 107 breast ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100573s
更新日期：2010-12-03 00:00:00
abstract：:Protein phosphatase 1 (PP1) catalytic subunits typically combine with other proteins that modulate their activity, direct them to distinct substrates, or serve as substrates for PP1. More than 50 PP1-interacting proteins (PIPs) have been identified so far. Given there are approximately 10 000 phosphoproteins in mammal...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060504h
更新日期：2007-03-01 00:00:00
abstract：:After tissue or body fluid sampling, proteases and other protein-modifying enzymes can rapidly change composition of the proteome. As a direct consequence, analytical results will reflect a mix of in vivo proteome and ex vivo degradation products. Vital information about the presampling state may be destroyed or disto...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr8006446
更新日期：2009-02-01 00:00:00
abstract：:Recombinant virus-like particles (VLPs) have been shown to induce protective immunity. Despite their potential significance as promising vaccine candidates, the protein composition of VLPs produced in insect cells has not been well characterized. Here we report a proteomic analysis of influenza VLPs containing hemaggl...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200086v
更新日期：2011-08-05 00:00:00
abstract：:Proteomics methods are being increasingly used to study archaeological and palaeontological bone, assisting in species identification and phylogenetic studies as well as improving our understanding of bone diagenesis. More recently, there are developing interests in the study of post-translational modifications, some ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00564
更新日期：2017-02-03 00:00:00
abstract：:Advances in liquid chromatography tandem mass spectrometry (LC-MS/MS) have permitted phosphoproteomic analysis on a grand scale, but ongoing challenges specifically associated with confident phosphate localization continue to motivate the development of new fragmentation techniques. In the present study, ultraviolet p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00289
更新日期：2016-08-05 00:00:00
abstract：:Protein chemical cross-linking combined with mass spectrometry has become an important technique for the analysis of protein structure and protein-protein interactions. A variety of cross-linkers are well developed, but reliable, rapid, and user-friendly tools for large-scale analysis of cross-linked proteins are stil...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00141
更新日期：2018-07-06 00:00:00
abstract：:We report the use of chemical derivatization with MALDI-MS/MS analysis for de novo sequence analysis. Using three frequently used homology-based search algorithms, we were able to identify more than 40 proteins from banana, a nonmodel plant with unsequenced genome. Furthermore, this approach allowed the identification...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0601943
更新日期：2007-01-01 00:00:00
abstract：:The protein kinase AKT is a central kinase in the heart and has a major impact on growth/hypertrophy, survival/apoptosis, and metabolism. To gain more insight into AKT isoform-specific signaling at the molecular level, we investigated the phosphoproteome of HL-1 cardiomyocytes carrying AKT1 or AKT2 isoform-specific kn...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500131g
更新日期：2014-10-03 00:00:00
abstract：:Trypanosoma cruzi is a protozoan that causes Chagas' disease, a neglected infectious illness that affects millions of people, mostly in Latin America. Here, the cell surface subproteome of the T. cruzi epimastigote life form was characterized. In order to prepare samples enriched in epimastigote plasma membrane protei...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400110h
更新日期：2013-07-05 00:00:00
abstract：:The bacterial ribosomal protein S12 contains a universally conserved D88 residue on a loop region thought to be critically involved in translation due to its proximal location to the A site of the 30S subunit. While D88 mutants are lethal this residue has been found to be post-translationally modified to β-methylthioa...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr3009435
更新日期：2013-03-01 00:00:00
abstract：:Human saliva is a protein-rich, easily accessible source of potential local and systemic biomarkers to monitor changes that occur under pathological conditions; however, little is known about the changes in abundance associated with normal aging. In this study, we performed a comprehensive proteomic profiling of poole...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900478h
更新日期：2009-11-01 00:00:00
