Identification of protein fragments as pattern features in MALDI-MS analyses of serum.

Zimmerman LJ, Wernke GR, Caprioli RM, Liebler DC
J Proteome Res. 2005 4 (5): 1672-80

PMID: 16212420 · DOI:10.1021/pr050138m

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.

MeSH Terms (14)

Algorithms Amino Acid Sequence Blood Proteins Chromatography, Liquid Colloids Electrophoresis, Polyacrylamide Gel Humans Molecular Sequence Data Peptide Mapping Peptides Proteins Proteome Proteomics Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

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