ArticleBMC bioinformatics2008
A robust linear regression based algorithm for automated evaluation of peptide identifications from shotgun proteomics by use of reversed-phase liquid chromatography retention time.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
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- Vesicle-based secretion in schistosomes: Analysis of protein and microRNA (miRNA) content of exosome-like vesicles derived from Schistosoma mansoni.Scientific reports · 2018Article
- The proteomic and metabolomic characterization of exercise-induced sweat for human performance monitoring: A pilot investigation.PloS one · 2018Article
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- Identification of replication-dependent and replication-independent linker histone complexes: Tpr specifically promotes replication-dependent linker histone stability.BMC biochemistry · 2016Article
- A multi-model statistical approach for proteomic spectral count quantitation.Journal of proteomics · 2016Article
- The chromatin scaffold protein SAFB1 localizes SUMO-1 to the promoters of ribosomal protein genes to facilitate transcription initiation and splicing.Nucleic acids research · 2015Article
- Direct identification of tyrosine sulfation by using ultraviolet photodissociation mass spectrometry.Journal of the American Society for Mass Spectrometry · 2014Article
- UV photodegradation of murine growth hormone: chemical analysis and immunogenicity consequences.European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V · 2014Article
- O18Quant: a semiautomatic strategy for quantitative analysis of high-resolution 16O/18O labeled data.BioMed research international · 2014Article
- Structure of the CRISPR interference complex CSM reveals key similarities with cascade.Molecular cell · 2013Article
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- Concurrent automated sequencing of the glycan and peptide portions of O-linked glycopeptide anions by ultraviolet photodissociation mass spectrometry.Analytical chemistry · 2013Article
- High-throughput database search and large-scale negative polarity liquid chromatography-tandem mass spectrometry with ultraviolet photodissociation for complex proteomic samples.Molecular & cellular proteomics : MCP · 2013Article
- Identification of oxidation sites and covalent cross-links in metal catalyzed oxidized interferon Beta-1a: potential implications for protein aggregation and immunogenicity.Molecular pharmaceutics · 2013Article
- Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities.Analytical chemistry · 2013Review
- Fluorogenic tagging methodology applied to characterize oxidized tyrosine and phenylalanine in an immunoglobulin monoclonal antibody.Pharmaceutical research · 2013Article
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3 authors.
Funding
Abstract
backgroundRejection of false positive peptide matches in database searches of shotgun proteomic experimental data is highly desirable. Several methods have been developed to use the peptide retention time as to refine and improve peptide identifications from database search algorithms. This report describes the implementation of an automated approach to reduce false positives and validate peptide matches.
resultsA robust linear regression based algorithm was developed to automate the evaluation of peptide identifications obtained from shotgun proteomic experiments. The algorithm scores peptides based on their predicted and observed reversed-phase liquid chromatography retention times. The robust algorithm does not require internal or external peptide standards to train or calibrate the linear regression model used for peptide retention time prediction. The algorithm is generic and can be incorporated into any database search program to perform automated evaluation of the candidate peptide matches based on their retention times. It provides a statistical score for each peptide match based on its retention time.
conclusionAnalysis of peptide matches where the retention time score was included resulted in a significant reduction of false positive matches with little effect on the number of true positives. Overall higher sensitivities and specificities were achieved for database searches carried out with MassMatrix, Mascot and X!Tandem after implementation of the retention time based score algorithm.
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