Nat Biotechnol. 2021 Dec;39(12):1563-1573. doi: 10.1038/s41587-021-00968-7. Epub 2021 Jul 08.

MaxDIA enables library-based and library-free data-independent acquisition proteomics.

Nature biotechnology

Pavel Sinitcyn, Hamid Hamzeiy, Favio Salinas Soto, Daniel Itzhak, Frank McCarthy, Christoph Wichmann, Martin Steger, Uli Ohmayer, Ute Distler, Stephanie Kaspar-Schoenefeld, Nikita Prianichnikov, Şule Yılmaz, Jan Daniel Rudolph, Stefan Tenzer, Yasset Perez-Riverol, Nagarjuna Nagaraj, Sean J Humphrey, Jürgen Cox

PMID: 34239088 DOI: 10.1038/s41587-021-00968-7

Abstract

MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves deep proteome coverage with substantially better coefficients of variation in protein quantification than other software. MaxDIA is equipped with accurate false discovery rate (FDR) estimates on both library-to-DIA match and protein levels, including when using whole-proteome predicted spectral libraries. This is the foundation of discovery DIA-hypothesis-free analysis of DIA samples without library and with reliable FDR control. MaxDIA performs three- or four-dimensional feature detection of fragment data, and scoring of matches is augmented by machine learning on the features of an identification. MaxDIA's bootstrap DIA workflow performs multiple rounds of matching with increasing quality of recalibration and stringency of matching to the library. Combining MaxDIA with two new technologies-BoxCar acquisition and trapped ion mobility spectrometry-both lead to deep and accurate proteome quantification.

© 2021. The Author(s).

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Publication Types

• Journal Article

Grant support

• FKZ 031L0214D/Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)
• FKZ 031L0217A/Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)
• SFB1292 Z02/Deutsche Forschungsgemeinschaft (German Research Foundation)