We present a tool to improve quantitative accuracy and precision in mass spectrometry based 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 due to the presence of different protein species. By correlation analysis, PQPQ 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 PQPQ 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.