Code developments to improve the efficiency of automated MS/MS spectra interpretation
- PMID: 12645897
- DOI: 10.1021/pr015514r
Code developments to improve the efficiency of automated MS/MS spectra interpretation
Abstract
We report the results of our work to facilitate protein identification using tandem mass spectra and protein sequence databases. We describe a parallel version of SEQUEST (SEQUEST-PVM) that is tolerant toward arithmetic exceptions. The changes we report effectively separate search processes on slave nodes from each other. Therefore, if one of the slave nodes drops out of the cluster due to an error, the rest of the cluster will carry the search process to the end. SEQUEST has been widely used for protein identifications. The modifications made to the code improve its stability and effectiveness in a high-throughput production environment. We evaluate the overhead associated with the parallelization of SEQUEST. A prior version of software to preprocess LC/MS/MS data attempted to differentiate the charge states of ions. Singly charged ions can be accurately identified, but the software was unable to reliably differentiate tandem mass spectra of +2 and +3 charge states. We have designed and implemented a computational approach to narrow charge states of precursor ions from nominal resolution ion-trap tandem mass spectra. The preprocessing code, 2to3, determines the charge state of the precursor ion using its mass-to-charge ratio (m/z) and fragment ions contained in the tandem mass spectrum. For each possible charge state the program calculates the expected fragment ions that account for precursor ion m/z values. If any one of the numbers is less than an empirically determined threshold value then the spectrum corresponding to that charge state is removed. If both numbers are higher than the threshold value then +2 and +3 copies of the spectrum are kept. We present the comparison of results from protein identification experiments with and without using 2 to 3. It is shown that by determining the charge state and eliminating poor quality spectra 2to3 decreases the number of spectral files to be searched without affecting the search results. The decrease reduces computer requirements and researcher efforts for analysis of the results.
Similar articles
-
Multiplexed and data-independent tandem mass spectrometry for global proteome profiling.Mass Spectrom Rev. 2014 Nov-Dec;33(6):452-70. doi: 10.1002/mas.21400. Epub 2013 Nov 26. Mass Spectrom Rev. 2014. PMID: 24281846 Review.
-
Clustering and filtering tandem mass spectra acquired in data-independent mode.J Am Soc Mass Spectrom. 2013 Dec;24(12):1862-71. doi: 10.1007/s13361-013-0720-z. Epub 2013 Sep 5. J Am Soc Mass Spectrom. 2013. PMID: 24006250
-
MAZIE: a mass and charge inference engine to enhance database searching of tandem mass spectra.J Am Soc Mass Spectrom. 2010 Jan;21(1):80-7. doi: 10.1016/j.jasms.2009.09.007. Epub 2009 Sep 17. J Am Soc Mass Spectrom. 2010. PMID: 19850495 Free PMC article.
-
Protein identification from product ion spectra of peptides validated by correlation between measured and predicted elution times in liquid chromatography/mass spectrometry.Proteomics. 2005 Mar;5(4):856-64. doi: 10.1002/pmic.200401047. Proteomics. 2005. PMID: 15668996
-
Ion/ion chemistry of high-mass multiply charged ions.Mass Spectrom Rev. 1998 Nov-Dec;17(6):369-407. doi: 10.1002/(SICI)1098-2787(1998)17:6<369::AID-MAS1>3.0.CO;2-J. Mass Spectrom Rev. 1998. PMID: 10360331 Review.
Cited by
-
Communication-avoiding micro-architecture to compute Xcorr scores for peptide identification.Int Conf Field Program Log Appl. 2021 Aug-Sep;2021:99-103. doi: 10.1109/fpl53798.2021.00024. Epub 2021 Oct 12. Int Conf Field Program Log Appl. 2021. PMID: 35440952 Free PMC article.
-
Quantitative transportomics identifies Kif5a as a major regulator of neurodegeneration.Elife. 2022 Mar 8;11:e68148. doi: 10.7554/eLife.68148. Elife. 2022. PMID: 35259089 Free PMC article.
-
Deep Learning-based MSMS Spectra Reduction in Support of Running Multiple Protein Search Engines on Cloud.Proceedings (IEEE Int Conf Bioinformatics Biomed). 2017 Nov;2017:1909-1914. doi: 10.1109/bibm.2017.8217951. Epub 2017 Dec 18. Proceedings (IEEE Int Conf Bioinformatics Biomed). 2017. PMID: 34430067 Free PMC article.
-
Cloudy with a Chance of Peptides: Accessibility, Scalability, and Reproducibility with Cloud-Hosted Environments.J Proteome Res. 2021 Apr 2;20(4):2076-2082. doi: 10.1021/acs.jproteome.0c00920. Epub 2021 Jan 29. J Proteome Res. 2021. PMID: 33513299 Free PMC article.
-
Temporal Quantitative Profiling of Newly Synthesized Proteins during Aβ Accumulation.J Proteome Res. 2021 Jan 1;20(1):763-775. doi: 10.1021/acs.jproteome.0c00645. Epub 2020 Nov 4. J Proteome Res. 2021. PMID: 33147027 Free PMC article.
MeSH terms
Substances
LinkOut - more resources
Other Literature Sources