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

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• 作者：Lisa J. Zimmerman ; Gregory R. Wernke ; Richard M. Caprioli ; and Daniel C. Liebler
• 刊名：Journal of Proteome Research
• 出版年：2005
• 出版时间：October 2005
• 年：2005
• 卷：4
• 期：5
• 页码：1672 - 1680
• 全文大小：301K
• 年卷期：v.4,no.5(October 2005)
• ISSN：1535-3907

文摘

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 subjected 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 MALDI LC-MS/MS bioinformatics proteolysis