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

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

doi:10.1038/s41587-021-00968-7

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

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^*

^*Corresponding author for this work

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Research output: Contribution to journal › Article › Academic › peer-review

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.

Original language	English
Pages (from-to)	1563-1573
Journal	Nature Biotechnology
Volume	39
DOIs	https://doi.org/10.1038/s41587-021-00968-7
Publication status	Published - Dec 2021
Externally published	Yes

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Sinitcyn, P., Hamzeiy, H., Soto, F. S., Itzhak, D., McCarthy, F., Wichmann, C., Steger, M., Ohmayer, U., Distler, U., Kaspar-Schoenefeld, S., Prianichnikov, N., Yılmaz, Ş., Rudolph, J. D., Tenzer, S., Perez-Riverol, Y., Nagaraj, N., Humphrey, S. J., & Cox, J. (2021). MaxDIA enables library-based and library-free data-independent acquisition proteomics. Nature Biotechnology, 39, 1563-1573. https://doi.org/10.1038/s41587-021-00968-7

@article{4c651a14b91246238f74c101e73d6bd9,

title = "MaxDIA enables library-based and library-free data-independent acquisition proteomics",

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{\textquoteright}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.",

author = "Pavel Sinitcyn and Hamid Hamzeiy and Soto, {Favio Salinas} and Daniel Itzhak and Frank McCarthy and Christoph Wichmann and Martin Steger and Uli Ohmayer and Ute Distler and Stephanie Kaspar-Schoenefeld and Nikita Prianichnikov and {\c S}ule Yılmaz and Rudolph, {Jan Daniel} and Stefan Tenzer and Yasset Perez-Riverol and Nagarjuna Nagaraj and Humphrey, {Sean J.} and J{\"u}rgen Cox",

year = "2021",

month = dec,

doi = "10.1038/s41587-021-00968-7",

language = "English",

volume = "39",

pages = "1563--1573",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Publishing Group",

}

Sinitcyn, P, Hamzeiy, H, Soto, FS, Itzhak, D, McCarthy, F, Wichmann, C, Steger, M, Ohmayer, U, Distler, U, Kaspar-Schoenefeld, S, Prianichnikov, N, Yılmaz, Ş, Rudolph, JD, Tenzer, S, Perez-Riverol, Y, Nagaraj, N, Humphrey, SJ & Cox, J 2021, 'MaxDIA enables library-based and library-free data-independent acquisition proteomics', Nature Biotechnology, vol. 39, pp. 1563-1573. https://doi.org/10.1038/s41587-021-00968-7

TY - JOUR

T1 - MaxDIA enables library-based and library-free data-independent acquisition proteomics

AU - Sinitcyn, Pavel

AU - Hamzeiy, Hamid

AU - Soto, Favio Salinas

AU - Itzhak, Daniel

AU - McCarthy, Frank

AU - Wichmann, Christoph

AU - Steger, Martin

AU - Ohmayer, Uli

AU - Distler, Ute

AU - Kaspar-Schoenefeld, Stephanie

AU - Prianichnikov, Nikita

AU - Yılmaz, Şule

AU - Rudolph, Jan Daniel

AU - Tenzer, Stefan

AU - Perez-Riverol, Yasset

AU - Nagaraj, Nagarjuna

AU - Humphrey, Sean J.

AU - Cox, Jürgen

PY - 2021/12

Y1 - 2021/12

N2 - 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.

AB - 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.

U2 - 10.1038/s41587-021-00968-7

DO - 10.1038/s41587-021-00968-7

M3 - Article

SN - 1087-0156

VL - 39

SP - 1563

EP - 1573

JO - Nature Biotechnology

JF - Nature Biotechnology

ER -

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

Abstract

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