MASH Native: a unified solution for native top-down proteomics data processing

Eli J. Larson; Melissa R. Pergande; Michelle E. Moss; Kalina J. Rossler; R. Kent Wenger; Boris Krichel; Harini Josyer; Jake A. Melby; David S. Roberts; Kyndalanne Pike; Zhuoxin Shi; Hsin Ju Chan; Bridget Knight; Holden T. Rogers; Kyle A. Brown; Irene M. Ong; Kyowon Jeong; Michael T. Marty; Sean J. McIlwain; Ying Ge

doi:10.1093/bioinformatics/btad359

MASH Native: a unified solution for native top-down proteomics data processing

Eli J. Larson
, Melissa R. Pergande
, Michelle E. Moss
, Kalina J. Rossler
, R. Kent Wenger
, Boris Krichel
, Harini Josyer
, Jake A. Melby
, David S. Roberts
, Kyndalanne Pike
, Zhuoxin Shi
, Hsin Ju Chan
, Bridget Knight
, Holden T. Rogers
, Kyle A. Brown
, Irene M. Ong
, Kyowon Jeong
, Michael T. Marty
, Sean J. McIlwain
, Ying Ge

Chemistry and Biochemistry

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

21 Scopus citations

Abstract

Motivation: Native top-down proteomics (nTDP) integrates native mass spectrometry (nMS) with top-down proteomics (TDP) to provide comprehensive analysis of protein complexes together with proteoform identification and characterization. Despite significant advances in nMS and TDP software developments, a unified and user-friendly software package for analysis of nTDP data remains lacking. Results: We have developed MASH Native to provide a unified solution for nTDP to process complex datasets with database searching capabilities in a user-friendly interface. MASH Native supports various data formats and incorporates multiple options for deconvolution, database searching, and spectral summing to provide a “one-stop shop” for characterizing both native protein complexes and proteoforms. Availability and implementation: The MASH Native app, video tutorials, written tutorials, and additional documentation are freely available for download at https://labs.wisc.edu/gelab/MASH_Explorer/MASHSoftware.php. All data files shown in user tutorials are included with the MASH Native software in the download .zip file.

Original language	English (US)
Article number	btad359
Journal	Bioinformatics
Volume	39
Issue number	6
DOIs	https://doi.org/10.1093/bioinformatics/btad359
State	Published - Jun 1 2023

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btad359

Cite this

Larson, E. J., Pergande, M. R., Moss, M. E., Rossler, K. J., Wenger, R. K., Krichel, B., Josyer, H., Melby, J. A., Roberts, D. S., Pike, K., Shi, Z., Chan, H. J., Knight, B., Rogers, H. T., Brown, K. A., Ong, I. M., Jeong, K., Marty, M. T., McIlwain, S. J., & Ge, Y. (2023). MASH Native: a unified solution for native top-down proteomics data processing. Bioinformatics, 39(6), Article btad359. https://doi.org/10.1093/bioinformatics/btad359

Larson, EJ, Pergande, MR, Moss, ME, Rossler, KJ, Wenger, RK, Krichel, B, Josyer, H, Melby, JA, Roberts, DS, Pike, K, Shi, Z, Chan, HJ, Knight, B, Rogers, HT, Brown, KA, Ong, IM, Jeong, K, Marty, MT, McIlwain, SJ & Ge, Y 2023, 'MASH Native: a unified solution for native top-down proteomics data processing', Bioinformatics, vol. 39, no. 6, btad359. https://doi.org/10.1093/bioinformatics/btad359

@article{d7ec9a9853d44e9baa2f66cb208c8f53,

title = "MASH Native: a unified solution for native top-down proteomics data processing",

abstract = "Motivation: Native top-down proteomics (nTDP) integrates native mass spectrometry (nMS) with top-down proteomics (TDP) to provide comprehensive analysis of protein complexes together with proteoform identification and characterization. Despite significant advances in nMS and TDP software developments, a unified and user-friendly software package for analysis of nTDP data remains lacking. Results: We have developed MASH Native to provide a unified solution for nTDP to process complex datasets with database searching capabilities in a user-friendly interface. MASH Native supports various data formats and incorporates multiple options for deconvolution, database searching, and spectral summing to provide a “one-stop shop” for characterizing both native protein complexes and proteoforms. Availability and implementation: The MASH Native app, video tutorials, written tutorials, and additional documentation are freely available for download at https://labs.wisc.edu/gelab/MASH\_Explorer/MASHSoftware.php. All data files shown in user tutorials are included with the MASH Native software in the download .zip file.",

author = "Larson, \{Eli J.\} and Pergande, \{Melissa R.\} and Moss, \{Michelle E.\} and Rossler, \{Kalina J.\} and Wenger, \{R. Kent\} and Boris Krichel and Harini Josyer and Melby, \{Jake A.\} and Roberts, \{David S.\} and Kyndalanne Pike and Zhuoxin Shi and Chan, \{Hsin Ju\} and Bridget Knight and Rogers, \{Holden T.\} and Brown, \{Kyle A.\} and Ong, \{Irene M.\} and Kyowon Jeong and Marty, \{Michael T.\} and McIlwain, \{Sean J.\} and Ying Ge",

note = "Publisher Copyright: {\textcopyright}The Author(s) 2023. Published by Oxford University Press.",

year = "2023",

month = jun,

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doi = "10.1093/bioinformatics/btad359",

language = "English (US)",

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T2 - a unified solution for native top-down proteomics data processing

AU - Larson, Eli J.

AU - Pergande, Melissa R.

AU - Moss, Michelle E.

AU - Rossler, Kalina J.

AU - Wenger, R. Kent

AU - Krichel, Boris

AU - Josyer, Harini

AU - Melby, Jake A.

AU - Roberts, David S.

AU - Pike, Kyndalanne

AU - Shi, Zhuoxin

AU - Chan, Hsin Ju

AU - Knight, Bridget

AU - Rogers, Holden T.

AU - Brown, Kyle A.

AU - Ong, Irene M.

AU - Jeong, Kyowon

AU - Marty, Michael T.

AU - McIlwain, Sean J.

AU - Ge, Ying

PY - 2023/6/1

Y1 - 2023/6/1

N2 - Motivation: Native top-down proteomics (nTDP) integrates native mass spectrometry (nMS) with top-down proteomics (TDP) to provide comprehensive analysis of protein complexes together with proteoform identification and characterization. Despite significant advances in nMS and TDP software developments, a unified and user-friendly software package for analysis of nTDP data remains lacking. Results: We have developed MASH Native to provide a unified solution for nTDP to process complex datasets with database searching capabilities in a user-friendly interface. MASH Native supports various data formats and incorporates multiple options for deconvolution, database searching, and spectral summing to provide a “one-stop shop” for characterizing both native protein complexes and proteoforms. Availability and implementation: The MASH Native app, video tutorials, written tutorials, and additional documentation are freely available for download at https://labs.wisc.edu/gelab/MASH_Explorer/MASHSoftware.php. All data files shown in user tutorials are included with the MASH Native software in the download .zip file.

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MASH Native: a unified solution for native top-down proteomics data processing

Abstract

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