About: Improved quality control processing of peptide-centric LC-MS proteomics data

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Improved quality control processing of peptide-centric LC-MS proteomics data
Creator	Baric, Ralph Webb-Robertson, Bobbie-Jo Sims, Amy Matzke, Melissa Jacobs, Jon Metz, Thomas Pounds, Joel Waters, Katrina
source	Medline; PMC
abstract	Motivation: In the analysis of differential peptide peak intensities (i.e. abundance measures), LC-MS analyses with poor quality peptide abundance data can bias downstream statistical analyses and hence the biological interpretation for an otherwise high-quality dataset. Although considerable effort has been placed on assuring the quality of the peptide identification with respect to spectral processing, to date quality assessment of the subsequent peptide abundance data matrix has been limited to a subjective visual inspection of run-by-run correlation or individual peptide components. Identifying statistical outliers is a critical step in the processing of proteomics data as many of the downstream statistical analyses [e.g. analysis of variance (ANOVA)] rely upon accurate estimates of sample variance, and their results are influenced by extreme values. Results: We describe a novel multivariate statistical strategy for the identification of LC-MS runs with extreme peptide abundance distributions. Comparison with current method (run-by-run correlation) demonstrates a significantly better rate of identification of outlier runs by the multivariate strategy. Simulation studies also suggest that this strategy significantly outperforms correlation alone in the identification of statistically extreme liquid chromatography-mass spectrometry (LC-MS) runs. Availability: https://www.biopilot.org/docs/Software/RMD.php Contact: bj@pnl.gov Supplementary information: Supplementary material is available at Bioinformatics online.
has issue date	2011-10-15(xsd:dateTime)
bibo:doi	10.1093/bioinformatics/btr479
bibo:pmid	21852304
has license	cc-by-nc
sha1sum (hex)	7aaaac381f47fcb8d47d69b810efd23a0db7bf15
schema:url	https://doi.org/10.1093/bioinformatics/btr479
resource representing a document's title	Improved quality control processing of peptide-centric LC-MS proteomics data
has PubMed Central identifier	PMC3187650
has PubMed identifier	21852304
schema:publication	Bioinformatics
resource representing a document's body	covid:7aaaac381f47fcb8d47d69b810efd23a0db7bf15#body_text
is schema:about of	named entity 'IMPROVED' named entity 'MEASURES' named entity 'PEAK' named entity 'SUGGEST' named entity 'METHOD' named entity 'VALUES' named entity 'INTERPRETATION' named entity 'ANALYSIS' named entity 'PEPTIDE IDENTIFICATION' named entity 'STATISTICAL ANALYSES' named entity 'QUALITY ASSESSMENT' named entity 'DIFFERENTIAL' named entity 'OUTLIER' named entity 'STRATEGY' named entity 'POOR QUALITY' named entity 'IDENTIFYING' named entity 'VISUAL INSPECTION' named entity 'COMPARISON' named entity 'QUALITY CONTROL' named entity 'STATISTICAL' named entity 'OUTLIERS' named entity 'PEPTIDE' named entity 'ACCURATE' named entity 'PROCESSING' named entity 'ABUNDANCE' named entity 'LIMITED' named entity 'PROTEOMICS' named entity 'PROCESSING' named entity 'DATA' named entity 'DISTRIBUTIONS' named entity 'BETTER' named entity 'SUBJECTIVE' named entity 'PLACED' named entity 'RESULTS' named entity 'IDENTIFICATION' named entity 'DESCRIBE' named entity 'DATE' named entity 'NOVEL' named entity 'HIGH' named entity 'DATASET' named entity 'SUBSEQUENT' named entity 'RATE' named entity 'ANALYSIS OF VARIANCE' named entity 'INDIVIDUAL' named entity 'RESPECT' named entity 'DATA MATRIX' named entity 'BIOLOGICAL' named entity '28I' named entity 'CONSIDERABLE' named entity 'CRITICAL STEP' named entity 'EXTREME' named entity 'RUNS' named entity 'THEIR' named entity 'DATA' named entity 'DOWNSTREAM' named entity 'GENE EXPRESSION' named entity 'LC-MS' named entity 'PEPTIDE' named entity 'CENTRIC' named entity 'INTENSITIES' named entity 'SPECTRAL' named entity 'ESTIMATES' named entity 'EFFORT' named entity 'SAMPLE VARIANCE' named entity 'IS A' named entity 'QUALITY' named entity 'CURRENT' named entity 'LC-MS' named entity 'SIMULATION' named entity 'RUN' named entity 'PROTEOMICS' named entity 'BIAS' named entity 'COMPONENTS' named entity 'CORRELATION'

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