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

Sinitcyn, P., Hamzeiy, H., Salinas Soto, F., Itzhak, D., McCarthy, F., Wichmann, C., et al. (2021). MaxDIA enables library-based and library-free data-independent acquisition proteomics. Nature Biotechnology, 39, 1563-1573. doi:10.1038/s41587-021-00968-7.

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Open access funding provided by Max Planck Institute of Biochemistry.
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 Creators:
Sinitcyn, Pavel1, Author           
Hamzeiy, Hamid1, Author           
Salinas Soto, Favio1, Author           
Itzhak, Daniel2, Author
McCarthy, Frank2, Author
Wichmann, Christoph1, Author           
Steger, Martin2, Author
Ohmayer, Uli2, Author
Distler, Ute2, Author
Kaspar-Schoenefeld, Stephanie2, Author
Prianichnikov, Nikita1, Author           
Yilmaz, Sule1, Author           
Rudolph, Jan Daniel1, Author           
Tenzer, Stefan2, Author
Perez-Riverol, Yasset2, Author
Nagaraj, Nagarjuna2, Author
Humphrey, Sean J.2, Author
Cox, Jürgen1, Author           
Affiliations:
1Cox, Jürgen / Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Max Planck Society, ou_2063284              
2external, ou_persistent22              

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Free keywords: LABEL-FREE QUANTIFICATION; PEPTIDE IDENTIFICATION; EXTRACTION; SOFTWARE; FORMAT; RATESBiotechnology & Applied Microbiology;
 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.
The software platform MaxDIA streamlines analysis of data-independent acquisition proteomics.

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Language(s): eng - English
 Dates: 2021
 Publication Status: Published in print
 Pages: 16
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
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Project name : Marie Skłodowska-Curie grant agreement
Grant ID : 792536
Funding program : Horizon 2020 (H2020)
Funding organization : European Commission (EC)

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Title: Nature Biotechnology
  Abbreviation : Nat. Biotechnol.
Source Genre: Journal
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Publ. Info: New York : Gale Group Inc.
Pages: - Volume / Issue: 39 Sequence Number: - Start / End Page: 1563 - 1573 Identifier: ISSN: 1087-0156
CoNE: https://pure.mpg.de/cone/journals/resource/954926980065