Chromatographic alignment improves differential MS

摘要

CRAWDAD software facilitates label-free quantitation of proteomics mixtures. Differential MS (dMS) can detect quantitative differences between samples without the need to label the analytes. However, variations in the LC retention times can complicate this method of label-free quantitation. To expand the applicability of dMS, Michael MacCoss and his colleagues at the University of Washington and the University of Colorado Denver have developed chromatogram retention-time alignment and warping for differential analysis of data (CRAWDAD), a new suite of software tools that aligns the LC/MS runs and then performs label-free quantitation of peptide mixtures with dMS (Anal. Chem. 2007, DOI 10.1021/ac701649e). Many researchers perform feature-based alignments, which apply a regression to match peaks or isotope clusters from the MS scan or peptide identities from the MS/MS scan. Instead, MacCoss and colleagues chose a signal-based alignment that breaks up the LC/MS run into bins of time and m/z and then optimizes the similarity scores between two runs through a dynamic time-warping algorithm. "Dynamic time warping is actually a pretty good technique for things that don't behave well, like chromatography," says Jacob Jaffe of the Broad Institute. After aligning LC/MS scans to a master scan, CRAWDAD identifies statistically significant regions of difference and checks whether the instrument acquired an MS/MS spectrum that can help identify the peptide.