You are here

Nat Methods DOI:10.1038/s41592-020-00986-4

Avant-garde: an automated data-driven DIA data curation tool.

Publication TypeJournal Article
Year of Publication2020
AuthorsJacome, ASebastian, Peckner, R, Shulman, N, Krug, K, DeRuff, KC, Officer, A, Christianson, KE, MacLean, B, MacCoss, MJ, Carr, SA, Jaffe, JD
JournalNat Methods
Volume17
Issue12
Pages1237-1244
Date Published2020 Dec
ISSN1548-7105
Abstract

Several challenges remain in data-independent acquisition (DIA) data analysis, such as to confidently identify peptides, define integration boundaries, remove interferences, and control false discovery rates. In practice, a visual inspection of the signals is still required, which is impractical with large datasets. We present Avant-garde as a tool to refine DIA (and parallel reaction monitoring) data. Avant-garde uses a novel data-driven scoring strategy: signals are refined by learning from the dataset itself, using all measurements in all samples to achieve the best optimization. We evaluate the performance of Avant-garde using benchmark DIA datasets and show that it can determine the quantitative suitability of a peptide peak, and reach the same levels of selectivity, accuracy, and reproducibility as manual validation. Avant-garde is complementary to existing DIA analysis engines and aims to establish a strong foundation for subsequent analysis of quantitative mass spectrometry data.

DOI10.1038/s41592-020-00986-4
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/33199889?dopt=Abstract

Alternate JournalNat Methods
PubMed ID33199889
PubMed Central IDPMC7723322
Grant ListU24-CA210979 / / U.S. Department of Health & Human Services | NIH | NCI | Division of Cancer Epidemiology and Genetics, National Cancer Institute (National Cancer Institute Division of Cancer Epidemiology and Genetics) /
U24-CA210986 / / U.S. Department of Health & Human Services | NIH | NCI | Division of Cancer Epidemiology and Genetics, National Cancer Institute (National Cancer Institute Division of Cancer Epidemiology and Genetics) /
U24 CA210986 / CA / NCI NIH HHS / United States
U54 HG008097 / HG / NHGRI NIH HHS / United States
U24 CA210979 / CA / NCI NIH HHS / United States
U01 CA214125 / CA / NCI NIH HHS / United States