title: Design and application of a data-independent precursor and product ion repository.
abstract: The functional design and application of a data-independent LC-MS precursor and product ion repository for protein identification, quantification, and validation is conceptually described. The ion repository was constructed from the sequence search results of a broad range of discovery experiments investigating various tissue types of two closely related mammalian species. The relative high degree of similarity in protein complement, ion detection, and peptide and protein identification allows for the analysis of normalized precursor and product ion intensity values, as well as standardized retention times, creating a multidimensional/orthogonal queryable, qualitative, and quantitative space. Peptide ion map selection for identification and quantification is primarily based on replication and limited variation. The information is stored in a relational database and is used to create peptide- and protein-specific fragment ion maps that can be queried in a targeted fashion against the raw or time aligned ion detections. These queries can be conducted either individually or as groups, where the latter affords pathway and molecular machinery analysis of the protein complement. The presented results also suggest that peptide ionization and fragmentation efficiencies are highly conserved between experiments and practically independent of the analyzed biological sample when using similar instrumentation. Moreover, the data illustrate only minor variation in ionization efficiency with amino acid sequence substitutions occurring between species. Finally, the data and the presented results illustrate how LC-MS performance metrics can be extracted and utilized to ensure optimal performance of the employed analytical workflows.
authors: Biological Sciences, University of Warwick, UK.
authors: Konstantinos
authors: K
authors: Thalassinos
authors: Johannes P C
authors: JP
authors: Vissers
authors: Stefan
authors: S
authors: Tenzer
authors: Yishai
authors: Y
authors: Levin
authors: J Will
authors: JW
authors: Thompson
authors: David
authors: D
authors: Daniel
authors: Darrin
authors: D
authors: Mann
authors: Mark R
authors: MR
authors: DeLong
authors: M Arthur
authors: MA
authors: Moseley
authors: Antoine H
authors: AH
authors: America
authors: Andrew K
authors: AK
authors: Ottens
authors: Greg S
authors: GS
authors: Cavey
authors: Georgios
authors: G
authors: Efstathiou
authors: James H
authors: JH
authors: Scrivens
authors: James I
authors: JI
authors: Langridge
authors: Scott J
authors: SJ
authors: Geromanos
mesh_terms: D002853:Chromatography, Liquid; D003628:Database Management Systems; D030562:Databases, Protein; D007477:Ions / Q000737:chemistry; D013058:Mass Spectrometry; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D007477:Ions; D010455:Peptides; D011506:Proteins