title: A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry.
abstract: We present a software tool for visualizing data obtained from analyzing complex peptide mixtures by liquid chromatography (LC) electrospray ionization (ESI) mass spectrometry (MS). The data are represented as a two-dimensional density plot. For experiments employing collision-induced dissociation (CID), links are embedded in the image to the CID spectra and the corresponding peptide sequences that are represented by the respective feature. The image provides an intuitive method to evaluate sample quality and the performance of an LC-ESI-MS system and can be used to optimize experimental conditions. Local patterns of the image can also be used to identify chemical contaminants and specific peptide features. Therefore, this software tool may have broad application in MS-based proteomics.
authors.affiliation: The Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103-8904, USA. xli@systemsbiology.org
authors.forename: Xiao-jun
authors.initials: XJ
authors.lastname: Li
authors.forename: Patrick G A
authors.initials: PG
authors.lastname: Pedrioli
authors.forename: Jimmy
authors.initials: J
authors.lastname: Eng
authors.forename: Dan
authors.initials: D
authors.lastname: Martin
authors.forename: Eugene C
authors.initials: EC
authors.lastname: Yi
authors.forename: Hookeun
authors.initials: H
authors.lastname: Lee
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods; D019992:Databases as Topic; D010455:Peptides / Q000032:analysis*; D012680:Sensitivity and Specificity; D012984:Software; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D013499:Surface Properties
chemical_list: D010455:Peptides