ArticleBioinformatics (Oxford, England)2018
SimPhospho: a software tool enabling confident phosphosite assignment.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Artificial Intelligence and Machine Learning in Mass Spectrometry-Based Proteomics and Metabolomics.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry.ACS measurement science au · 2024Review
- Computational approaches to identify sites of phosphorylation.Proteomics · 2024Review
- Article
- A Multipathway Phosphopeptide Standard for Rapid Phosphoproteomics Assay Development.Molecular & cellular proteomics : MCP · 2023Article
- A multi-purpose, regenerable, proteome-scale, human phosphoserine resource for phosphoproteomics.Nature methods · 2022Article
- Optimization of TripleTOF spectral simulation and library searching for confident localization of phosphorylation sites.PloS one · 2019Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: Mass spectrometry combined with enrichment strategies for phosphorylated peptides has been successfully employed for two decades to identify sites of phosphorylation. However, unambiguous phosphosite assignment is considered challenging. Given that site-specific phosphorylation events function as different molecular switches, validation of phosphorylation sites is of utmost importance. In our earlier study we developed a method based on simulated phosphopeptide spectral libraries, which enables highly sensitive and accurate phosphosite assignments. To promote more widespread use of this method, we here introduce a software implementation with improved usability and performance. Results: We present SimPhospho, a fast and user-friendly tool for accurate simulation of phosphopeptide tandem mass spectra. Simulated phosphopeptide spectral libraries are used to validate and supplement database search results, with a goal to improve reliable phosphoproteome identification and reporting. The presented program can be easily used together with the Trans-Proteomic Pipeline and integrated in a phosphoproteomics data analysis workflow. Availability and implementation: SimPhospho is open source and it is available for Windows, Linux and Mac operating systems. The software and its user's manual with detailed description of data analysis as well as test data can be found at https://sourceforge.net/projects/simphospho/. Supplementary information: Supplementary data are available at Bioinformatics online.
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