ArticleBMC bioinformatics2018
Accelerating a cross-correlation score function to search modifications using a single GPU.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
3 citing papers in PubMed.
- MotifQuest: An Automated Pipeline for Motif Database Creation to Improve Peptidomics Database Searching Programs.Journal of the American Society for Mass Spectrometry · 2024Article
- GPU-acceleration of the distributed-memory database peptide search of mass spectrometry data.Scientific reports · 2023Article
- Identification of Splice Variants and Isoforms in Transcriptomics and Proteomics.Annual review of biomedical data science · 2023Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA cross-correlation (XCorr) score function is one of the most popular score functions utilized to search peptide identifications in databases, and many computer programs, such as SEQUEST, Comet, and Tide, currently use this score function. Recently, the HiXCorr algorithm was developed to speed up this score function for high-resolution spectra by improving the preprocessing step of the tandem mass spectra. However, despite the development of the HiXCorr algorithm, the score function is still slow because candidate peptides increase when post-translational modifications (PTMs) are considered in the search.
resultsWe used a graphics processing unit (GPU) to develop the accelerating score function derived by combining Tide's XCorr score function and the HiXCorr algorithm. Our method is 2.7 and 5.8 times faster than the original Tide and Tide-Hi, respectively, for 50 Da precursor tolerance. Our GPU-based method produced identical scores as did the CPU-based Tide and Tide-Hi.
conclusionWe propose the accelerating score function to search modifications using a single GPU. The software is available at https://github.com/Tide-for-PTM-search/Tide-for-PTM-search .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.