The use of matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) to acquirespectral 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 proteinsHere, 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 fragmentsconsistent with both types of data. This approach was used to identify protein fragments correspondingto spectral signals in MALDI-MS analyses of unfractionated human serum. The serum also was analyzedby one-dimensional SDS-PAGE and bands corresponding to the MALDI-MS signal masses were excisedand sub
jected to in-gel digestion and LC-MS/MS analysis. Database searches mapped all of theidentified peptides to abundant blood proteins larger than the observed MALDI-MS signals. FragMintidentified fragments of these proteins that contained the MS/MS identified sequences and wereconsistent with the observed MALDI-MS signals. This approach should be generally applicable toidentify protein species corresponding to MALDI-MS signals.Keywords: serum
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MALDI
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LC-MS/MS
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bioinformatics
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proteolysis