Data Dependent-Independent Acquisition (DDIA) Proteomics.

Journal of Proteome Research
Shenheng GuanBin Ma

Abstract

Data dependent acquisition (DDA) and data independent acquisition (DIA) are traditionally separate experimental paradigms in bottom-up proteomics. In this work, we developed a strategy combining the two experimental methods into a single LC-MS/MS run. We call the novel strategy data dependent-independent acquisition proteomics, or DDIA for short. Peptides identified from DDA scans by a conventional and robust DDA identification workflow provide useful information for interrogation of DIA scans. Deep learning based LC-MS/MS property prediction tools, developed previously, can be used repeatedly to produce spectral libraries facilitating DIA scan extraction. A complete DDIA data processing pipeline, including the modules for iRT vs RT calibration curve generation, DIA extraction classifier training, and false discovery rate control, has been developed. Compared to another spectral library-free method, DIA-Umpire, the DDIA method produced a similar number of peptide identifications, but nearly twice as many protein group identifications. The primary advantage of the DDIA method is that it requires minimal information for processing its data.

References

Sep 23, 2011·Molecular & Cellular Proteomics : MCP·Shenheng GuanAlma L Burlingame
Jul 4, 2013·Molecular & Cellular Proteomics : MCP·Nicholas W BatemanChristine C Wu
Nov 2, 2014·Nature Communications·Sangtae Kim, Pavel A Pevzner
Jan 20, 2015·Nature Methods·Chih-Chiang TsouAlexey I Nesvizhskii
Nov 10, 2015·Nature Methods·Jian WangNuno Bandeira
Feb 12, 2017·Methods in Molecular Biology·Hannes L RöstOlga T Schubert
Jul 12, 2017·Mass Spectrometry Reviews·Lindsay K PinoMichael J MacCoss
Sep 6, 2017·PLoS Computational Biology·Minseung KimIlias Tagkopoulos
Aug 15, 2018·Molecular Systems Biology·Christina LudwigRuedi Aebersold
Nov 6, 2018·Molecular & Cellular Proteomics : MCP·Florian MeierMatthias Mann
May 28, 2019·Nature Methods·Siegfried GessulatMathias Wilhelm
Feb 6, 2020·Journal of Proteome Research·Johra Muhammad MoosaBin Ma
Oct 1, 2019·Molecular & Cellular Proteomics : MCP·Shenheng GuanBin Ma

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Citations

Mar 7, 2021·International Journal of Molecular Sciences·Natalie TurnerMurray D Mitchell
Dec 4, 2021·Mass Spectrometry Reviews·Ágnes RévészLászló Drahos

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