TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization
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Summary: Top-down mass spectrometry enables the observation of whole complex proteoforms in biological samples and provides crucial information complementary to bottom-up mass spectrometry. Because of the complexity of top-down mass spectra and proteoforms, it is a challenging problem to efficiently interpret top-down tandem mass spectra in high-throughput proteome-level proteomics studies. We present TopPIC, a tool that efficiently identifies and characterizes complex proteoforms with unknown primary structure alterations, such as amino acid mutations and post-translational modifications, by searching top-down tandem mass spectra against a protein database. Availability and Implementation: http://proteomics.informatics.iupui.edu/software/toppic/ Contact: xwliu@iupui.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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MASH Explorer incorporates multiple database search algorithms, including MS-Align+, TopPIC, pTop, and MSPathFinderT.
“The database search algorithms such as MS-Align+,18 TopPIC,14 pTop,15 and MSPathFinderT26 were integrated in the software for protein identification.”
From MASH Explorer: A Universal Software Environment for Top-Down Proteomics (2020) · cites this paper as [14]
MASH Explorer incorporates multiple deconvolution algorithms, including MS-Deconv, TopFD, eTHRASH, pParseTD, and ProMex.
“Currently, the software incorporates various deconvolution algorithms including MS-Deconv,17 TopFD,14 eTHRASH,19 pParseTD,15 and ProMex26 for both MS and MS/MS deconvolution.”
From MASH Explorer: A Universal Software Environment for Top-Down Proteomics (2020) · cites this paper as [14]
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- Authors
- Kou, Q., Xun, L., & Liu, X.
- Affiliations
- Indiana University – Purdue University Indianapolis (US)
- Indiana University Indianapolis (US)
- Corresponding author
- Liu, Xiaowen
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-07-16
- Volume
- 32
- Issue
- 22
- Pages
- 3495-3497
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC5181555
- OpenAlex
- W2462197865
- Cited by
- 276
- References
- 12
- Citations by year
- 2026: 31 · 2025: 39 · 2024: 35 · 2023: 33 · 2022: 29 · 2021: 31 · 2020: 23 · 2019: 21 · 2018: 17 · 2017: 13 · 2016: 4
- FWCI
- 9.14
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- IUScholarWorks (Indiana University) (submittedVersion)
- Purdue University Indianapolis (Indiana University) (submittedVersion)
- PMC
- Funders
- National Institute of General Medical Sciences
- National Institutes of Health (R01GM118470)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- top-down mass spectrometry, proteoform identification, protein database search, post-translational modification, amino acid mutations, proteomics software
- MeSH terms
- Animals, Humans, Protein Processing, Post-Translational, Software, Proteome, Proteomics, Tandem Mass Spectrometry
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