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Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-Independent Acquisition Mass Spectrometry.

Type Information
Nr 51 (Research article)
Authors Parker, Sarah; Roest, Hannes; Rosenberger, George; Collins, Ben; Malmström, Lars; Amodei, Dario; Venkatraman, Vidya; Raedschelders, Koen; Van Eyk, Jennifer; Aebersold, Ruedi
Title Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-Independent Acquisition Mass Spectrometry.
Journal Mol Cell Proteomics (2015) 14(10) 2800-13
DOI 10.1074/mcp.O114.042267
Citations 45 citations (journal impact: 7.25)
Abstract Accurate knowledge of retention time RT in liquid chromatography-based mass spectrometry data facilitates peptide identification quantification and multiplexing in targeted and discovery-based workflows. Retention time prediction is particularly important for peptide analysis in emerging data-independent acquisition DIA experiments such as SWATH-MS. The indexed RT approach iRT uses synthetic spiked-in peptide standards SiRT to set RT to a unit-less scale allowing for normalization of peptide RT between different samples and chromatographic set-ups. The obligatory use of SiRTs can be costly and complicates comparisons and data integration if standards are not included in every sample. Reliance on SiRTs also prevents the inclusion of archived mass spectrometry data for generation of the peptide assay libraries central to targeted DIA-MS data analysis. We have identified a set of peptide sequences that are conserved across most eukaryotic species termed Common internal Retention Time standards CiRT. In a series of tests to support the appropriateness of the CiRT-based method we show 1 the CiRT peptides normalized RT in human yeast and mouse cell lysate derived peptide assay libraries and enabled merging of archived libraries for expanded DIA-MS quantitative applications 2 CiRTs predicted RT in SWATH-MS data within a 2-minute margin of error for the majority of peptides and 3 normalization of RT using the CiRT peptides enabled the accurate SWATH-MS-based quantification of 340 synthetic isotopically labeled peptides that were spiked into either human or yeast cell lysate. To automate and facilitate the use of these CiRT peptide lists or other custom user-defined internal RT reference peptides in DIA workflows an algorithm was designed to automatically select a high-quality subset of data points for robust linear alignment of RT for use. Implementations of this algorithm are available for the OpenSWATH and Skyline platforms. Thus CiRT peptides can be used alone or as a complement to SiRTs for RT normalization across peptide spectral libraries and in quantitative DIA-MS studies.