title: Enhanced information output from shotgun proteomics data by protein quantification and peptide quality control (PQPQ).
abstract: We present a tool to improve quantitative accuracy and precision in mass spectrometry based on shotgun proteomics: protein quantification by peptide quality control, PQPQ. The method is based on the assumption that the quantitative pattern of peptides derived from one protein will correlate over several samples. Dissonant patterns arise either from outlier peptides or because of the presence of different protein species. By correlation analysis, protein quantification by peptide quality control identifies and excludes outliers and detects the existence of different protein species. Alternative protein species are then quantified separately. By validating the algorithm on seven data sets related to different cancer studies we show that data processing by protein quantification by peptide quality control improves the information output from shotgun proteomics. Data from two labeling procedures and three different instrumental platforms was included in the evaluation. With this unique method using both peptide sequence data and quantitative data we can improve the quantitative accuracy and precision on the protein level and detect different protein species.
authors: The Science for Life Laboratory Stockholm and Department of Oncology-Pathology, Mass spectrometry and Proteomics, Science for Life Laboratory, Box 1031, 17121 Solna, Sweden. jenny.forshed@ki.se
authors: Jenny
authors: J
authors: Forshed
authors: Henrik J
authors: HJ
authors: Johansson
authors: Maria
authors: M
authors: Pernemalm
authors: Rui M M
authors: RM
authors: Branca
authors: Annsofi
authors: A
authors: Sandberg
authors: Janne
authors: J
authors: Lehtiö
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D002853:Chromatography, Liquid; D030562:Databases, Protein; D006801:Humans; D007553:Isotope Labeling; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000032:analysis* / Q000378:metabolism*; D011506:Proteins / Q000032:analysis* / Q000378:metabolism*; D040901:Proteomics; D011786:Quality Control; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D013223:Statistics as Topic / Q000379:methods; D053719:Tandem Mass Spectrometry
chemical_list: D010455:Peptides; D011506:Proteins