title: Identification of protein fragments as pattern features in MALDI-MS analyses of serum.
abstract: 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.
authors.affiliation: Departments of Biochemistry and Pharmacology and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, 9160 Medical Research Building III, 465 21st Avenue South, Nashville, TN 37232, USA. lisa.j.zimmerman@vanderbilt.edu
authors.forename: Lisa J
authors.initials: LJ
authors.lastname: Zimmerman
authors.forename: Gregory R
authors.initials: GR
authors.lastname: Wernke
authors.forename: Richard M
authors.initials: RM
authors.lastname: Caprioli
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Liebler
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001798:Blood Proteins / Q000737:chemistry*; D002853:Chromatography, Liquid; D003102:Colloids / Q000494:pharmacology; D004591:Electrophoresis, Polyacrylamide Gel; D006801:Humans; D008969:Molecular Sequence Data; D010449:Peptide Mapping; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*
chemical_list: D001798:Blood Proteins; D003102:Colloids; D010455:Peptides; D011506:Proteins; D020543:Proteome