Identification of Protein Fragments as Pattern Features in MALDI−MS Analyses of Serum

The use of matrix-assisted laser desorption ionization mass spectrometry (MALDI−MS) to acquire spectral profiles has become a common approach to detect proteomic biomarkers of disease. MALDI−MS signals may represent both intact proteins as well as proteolysis products. Liquid chromatography-tandem mass spectrometry (LC−MS/MS) analysis can tentatively identify the corresponding proteins Here, we describe the application of a data analysis utility called FragMint, which combines MALDI−MS spectral data with LC−MS/MS based protein identifications to generate candidate protein fragments consistent with both types of data. This approach was used to identify protein fragments corresponding to spectral signals in MALDI−MS analyses of unfractionated human serum. The serum also was analyzed by one-dimensional SDS-PAGE and bands corresponding to the MALDI−MS signal masses were excised and subjected to in-gel digestion and LC−MS/MS analysis. Database searches mapped all of the identified peptides to abundant blood proteins larger than the observed MALDI−MS signals. FragMint identified fragments of these proteins that contained the MS/MS identified sequences and were consistent with the observed MALDI−MS signals. This approach should be generally applicable to identify protein species corresponding to MALDI−MS signals. Keywords: serum • MALDI • LC−MS/MS • bioinformatics • proteolysis