title: Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS V2.0.
abstract: The Virtual Expert Mass Spectrometrist (VEMS) program package was developed for flexible, automated, and manual de novo tandem mass spectrometry (MS/MS) protein sequencing, and includes accessory programs for matrix-assisted laser desorption/ionization-mass spectrometry (MS) interpretation, and generation of protein and peptide databases. VEMS V2.0 has been developed into a fast tool for combining database-independent and -dependent protein assignments in an extended analysis of MS/MS-peptide data. MS or MS/MS data can be directly recalibrated after the first search by fitting the data to the best search result using polynomial equations. The score function is an improvement of known scoring algorithms and can be adapted for any MS instrument type. In addition, VEMS offers a novel statistical model for evaluating the significance of the protein assignment. The novel features are illustrated by the analysis of the fragmentation spectra obtained by liquid chromatrography-MS/MS analysis of peptides from an anionic peroxidase enriched protein fraction from potato root tissue. The extended analysis mode resulted in the additional assignment of spectra for nine modified tryptic peptides and nine miscleaved peptides, in addition to the 45 spectra from regular tryptic peptides. Of the nine modified peptides, three were glycosylated.
authors.affiliation: Department of Life Sciences, Aalborg University, Aalborg, Denmark.
authors.forename: Rune
authors.initials: R
authors.lastname: Matthiesen
authors.forename: Jakob
authors.initials: J
authors.lastname: Bunkenborg
authors.forename: Allan
authors.initials: A
authors.lastname: Stensballe
authors.forename: Ole N
authors.initials: ON
authors.lastname: Jensen
authors.forename: Karen G
authors.initials: KG
authors.lastname: Welinder
authors.forename: Guy
authors.initials: G
authors.lastname: Bauw
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D002240:Carbohydrate Sequence; D030562:Databases, Protein; D013058:Mass Spectrometry / Q000295:instrumentation* / Q000379:methods*; D008969:Molecular Sequence Data; D010455:Peptides / Q000032:analysis*; D010936:Plant Extracts / Q000737:chemistry; D010940:Plant Proteins / Q000737:chemistry / Q000378:metabolism; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D011198:Solanum tuberosum / Q000737:chemistry
chemical_list: D010455:Peptides; D010936:Plant Extracts; D010940:Plant Proteins