title: MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics.
abstract: Top-down mass spectrometry (MS)-based proteomics is arguably a disruptive technology for the comprehensive analysis of all proteoforms arising from genetic variation, alternative splicing, and posttranslational modifications (PTMs). However, the complexity of top-down high-resolution mass spectra presents a significant challenge for data analysis. In contrast to the well-developed software packages available for data analysis in bottom-up proteomics, the data analysis tools in top-down proteomics remain underdeveloped. Moreover, despite recent efforts to develop algorithms and tools for the deconvolution of top-down high-resolution mass spectra and the identification of proteins from complex mixtures, a multifunctional software platform, which allows for the identification, quantitation, and characterization of proteoforms with visual validation, is still lacking. Herein, we have developed MASH Suite Pro, a comprehensive software tool for top-down proteomics with multifaceted functionality. MASH Suite Pro is capable of processing high-resolution MS and tandem MS (MS/MS) data using two deconvolution algorithms to optimize protein identification results. In addition, MASH Suite Pro allows for the characterization of PTMs and sequence variations, as well as the relative quantitation of multiple proteoforms in different experimental conditions. The program also provides visualization components for validation and correction of the computational outputs. Furthermore, MASH Suite Pro facilitates data reporting and presentation via direct output of the graphics. Thus, MASH Suite Pro significantly simplifies and speeds up the interpretation of high-resolution top-down proteomics data by integrating tools for protein identification, quantitation, characterization, and visual validation into a customizable and user-friendly interface. We envision that MASH Suite Pro will play an integral role in advancing the burgeoning field of top-down proteomics.
authors.affiliation: From the ‡Department of Cell and Regenerative Biology, §Molecular Pharmacology Training Program.
authors.forename: Wenxuan
authors.initials: W
authors.lastname: Cai
authors.affiliation: From the ‡Department of Cell and Regenerative Biology, ¶Human Proteomics Program.
authors.forename: Huseyin
authors.initials: H
authors.lastname: Guner
authors.affiliation: From the ‡Department of Cell and Regenerative Biology, §Molecular Pharmacology Training Program.
authors.forename: Zachery R
authors.initials: ZR
authors.lastname: Gregorich
authors.affiliation: From the ‡Department of Cell and Regenerative Biology.
authors.forename: Albert J
authors.initials: AJ
authors.lastname: Chen
authors.affiliation: From the ‡Department of Cell and Regenerative Biology.
authors.forename: Serife
authors.initials: S
authors.lastname: Ayaz-Guner
authors.affiliation: From the ‡Department of Cell and Regenerative Biology.
authors.forename: Ying
authors.initials: Y
authors.lastname: Peng
authors.affiliation: From the ‡Department of Cell and Regenerative Biology.
authors.forename: Santosh G
authors.initials: SG
authors.lastname: Valeja
authors.affiliation: **Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 West 10th Street, Indianapolis, IN 46202.
authors.forename: Xiaowen
authors.initials: X
authors.lastname: Liu
authors.affiliation: From the ‡Department of Cell and Regenerative Biology, ¶Human Proteomics Program, ‡‡Department of Chemistry, University of Wisconsin-Madison, 1300 University Ave., Madison, WI 53706,Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Indiana Ave., Indianapolis, IN 46202, ge2@wisc.edu.
authors.forename: Ying
authors.initials: Y
authors.lastname: Ge
mesh_terms: D000465:Algorithms; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000235:genetics*; D040901:Proteomics / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry
chemical_list: D020543:Proteome