PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios

We have developed Peptide Profiling Guided Identification of Proteins (PPINGUIN), a statistical analysis workflow for iTRAQ data addressing the problem of ambiguous peptide quantitations. Motivated by the assumption that peptides uniquely derived from the same protein are correlated, our method employs clustering as a very early step in data processing prior to protein inference. Our method increases experimental reproducibility and decreases variability of quantitations of peptides assigned to the same protein. Giving further support to our method, application to a type 2 diabetes dataset identifies a list of protein candidates that is in very good agreement with previously performed transcriptomics meta analysis. Making use of quantitative properties of signal patterns identified, PPINGUIN can reveal new isoform candidates.Regarding the increasing importance of quantitative proteomics we think that this method will be useful in practical applications like model fitting or functional enrichment analysis. We recommend to use this method if quantitation is a major objective of research.Quantitative proteomics is becoming increasingly important and over the last years many efforts have been made to develop and improve methods allowing for protein quantification. Besides gel based approaches [1,2], mass spectral techniques encompassing labeling techniques such as iTRAQ [3], ICAT [4] and SILAC [5,6] as well as label free approaches are widely-used for quantitative proteomics. Especially iTRAQ (isobaric tags for relative and absolute quantitation) gained much popularity as it allows for multiplexing quantitation of up to 8 samples. This new flexibility has been used recently in several studies investigating various objectives [7-11].Complementing these experimental technologies, a wide range of quantification algorithms can be found in the literature. The most common algorithms are included in software packages such as MASCOT, ProQUANT, i-TRACKER [12,13], Multi-Q [14] or