Semi-supervised learning for peptide identification from shotgun proteomics datasets
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Summary
An algorithm, called Percolator, is described, for improving the rate of confident peptide identifications from a collection of tandem mass spectra, using semi-supervised machine learning to discriminate between correct and decoy spectrum identifications.
- Type
- article
- Published
- 2007-11-01
- Cited by
- 2,214
- References
- 27
- OpenAlex
- https://openalex.org/W2053943711
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:2539384
Keywords
Shotgun proteomics, Shotgun, Proteomics, Tandem mass spectrometry, Identification (biology)
References
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- Probability-based validation of protein identifications using a modified SEQUEST algorithm.
- InsPecT: identification of posttranslationally modified peptides from tandem mass spectra.
- A training algorithm for optimal margin classifiers
- Qscore: An algorithm for evaluating SEQUEST database search results
- A Modified Finite Newton Method for Fast Solution of Large Scale Linear SVMs
- Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.
- Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries.
- Peptide charge state determination for low-resolution tandem mass spectra
- Large scale semi-supervised linear SVMs
- Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome.
Cited by
- Target-Decoy Search Strategy for Mass Spectrometry-Based Proteomics
- Current algorithmic solutions for peptide-based proteomics data generation and identification
- An automated pipeline for high-throughput label-free quantitative proteomics.
- Proteomic tools for environmental microbiology—A roadmap from sample preparation to protein identification and quantification
- LTQ-XL mass spectrometry proteome analysis expands the Pseudomonas aeruginosa AmpR regulon to include cyclic di-GMP phosphodiesterases and phosphoproteins, and identifies novel open reading frames
- The interactome of the atypical phosphatase Rtr1 in Saccharomyces cerevisiae
- Ion Mobility Tandem Mass Spectrometry Enhances Performance of Bottom-up Proteomics
- Custom 4-Plex DiLeu Isobaric Labels Enable Relative Quantification of Urinary Proteins in Men with Lower Urinary Tract Symptoms (LUTS)
- Data from proteomic characterization of the role of Snail1 in murine mesenchymal stem cells and 3T3-L1 fibroblasts differentiation
- Proteomic profile of platelets during reconstitution of platelet counts after apheresis
- Predictive chromatography of peptides and proteins as a complementary tool for proteomics.
- Proteogenomics: Key Driver for Clinical Discovery and Personalized Medicine.
- A tyrosine kinase-STAT5-miR21-PDCD4 regulatory axis in chronic and acute myeloid leukemia cells
- pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization.
- Quantitative evolutionary proteomics of seminal fluid from primates with different mating systems
- An investigation of CD147 expression in apoptotic vesicles
- Mass spectrometry-driven proteomics: an introduction.
- Bioinformatics for LC-MS/MS-based proteomics.
- The accuracy of statistical confidence estimates in shotgun proteomics
- Semi-supervised and transductive learning algorithms for predicting alternative splicing events in genes.
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