MassAnalyzer, a program to help find labeled peptides and compare them to their unlabeled counterparts in a SILAC experiment

Abstract

Mass spectrometry(MS) have become an increasingly popular analysis method for high throughput experiments on proteins in biology. SILAC(stable isotope labeling by amino acids in cell culture) is a method within MS that uses labels to differentiate between the same protein from two cell cultures(protein pairs) of the same organism. To identify the protein pairs in SILAC MS/MS is used. The current/automatic method for MS/MS uses the most intense peaks from each single MS for the MS/MS analysis. This often result in incomplete pairs, and proteins that have a low abundance gets ignored. We created a program able to identify these pairs, and the researcher can use the data from it as an inclusion list for the MS/MS run. The program should be easy to maintain and use for other MS data analysis.