title: A platform for accurate mass and time analyses of mass spectrometry data.
abstract: We describe an integrated suite of algorithms and software for general accurate mass and time (AMT) tagging data analysis of mass spectrometry data. The AMT approach combines identifications from liquid chromatography (LC) tandem mass spectrometry (MS/MS) data with peptide accurate mass and retention time locations from high-resolution LC-MS data. Our workflow includes the traditional AMT approach, in which MS/MS identifications are located in external databases, as well as methods based on more recent hybrid instruments such as the LTQ-FT or Orbitrap, where MS/MS identifications are embedded with the MS data. We demonstrate our AMT workflow's utility for general data synthesis by combining data from two dissimilar biospecimens. Specifically, we demonstrate its use relevant to serum biomarker discovery by identifying which peptides sequenced by MS/MS analysis of tumor tissue may also be present in the plasma of tumor-bearing and control mice. The analysis workflow, referred to as msInspect/AMT, extends and combines existing open-source platforms for LC-MS/MS (CPAS) and LC-MS (msInspect) data analysis and is available in an unrestricted open-source distribution.
authors.affiliation: Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
authors.forename: Damon
authors.initials: D
authors.lastname: May
authors.forename: Matt
authors.initials: M
authors.lastname: Fitzgibbon
authors.forename: Yan
authors.initials: Y
authors.lastname: Liu
authors.forename: Ted
authors.initials: T
authors.lastname: Holzman
authors.forename: Jimmy
authors.initials: J
authors.lastname: Eng
authors.forename: C J
authors.initials: CJ
authors.lastname: Kemp
authors.forename: Jeff
authors.initials: J
authors.lastname: Whiteaker
authors.forename: Amanda
authors.initials: A
authors.lastname: Paulovich
authors.forename: Martin
authors.initials: M
authors.lastname: McIntosh
mesh_terms: D000465:Algorithms; D000818:Animals; D015415:Biomarkers / Q000097:blood; D002853:Chromatography, Liquid; D030562:Databases, Protein; D001330:Electronic Data Processing; D013058:Mass Spectrometry; D051379:Mice; D010455:Peptides / Q000032:analysis*; D012984:Software; D018511:Systems Integration
chemical_list: D015415:Biomarkers; D010455:Peptides