Current trends in computational inference from mass spectrometry-based proteomics
- PMID: 17584764
- DOI: 10.1093/bib/bbm023
Current trends in computational inference from mass spectrometry-based proteomics
Abstract
Mass spectrometry offers a high-throughput approach to quantifying the proteome associated with a biological sample and hence has become the primary approach of proteomic analyses. Computation is tightly coupled to this advanced technological platform as a required component of not only peptide and protein identification, but quantification and functional inference, such as protein modifications and interactions. Proteomics faces several key computational challenges such as identification of proteins and peptides from tandem mass spectra as well as their quantitation. In addition, the application of proteomics to systems biology requires understanding the functional proteome, including how the dynamics of the cell change in response to protein modifications and complex interactions between biomolecules. This review presents an overview of recently developed methods and their impact on these core computational challenges currently facing proteomics.
Similar articles
-
Mass spectrometry in systems biology: an overview.Mass Spectrom Rev. 2008 Nov-Dec;27(6):635-60. doi: 10.1002/mas.20182. Mass Spectrom Rev. 2008. PMID: 18636545 Review.
-
Phosphoproteomics by mass spectrometry and classical protein chemistry approaches.Mass Spectrom Rev. 2005 Nov-Dec;24(6):828-46. doi: 10.1002/mas.20042. Mass Spectrom Rev. 2005. PMID: 15538747 Review.
-
Latest developments in sample treatment for 18O-isotopic labeling for proteomics mass spectrometry-based approaches: a critical review.Talanta. 2010 Feb 15;80(4):1476-86. doi: 10.1016/j.talanta.2009.04.053. Epub 2009 May 4. Talanta. 2010. PMID: 20082805
-
A review of current applications of mass spectrometry for neuroproteomics in epilepsy.Mass Spectrom Rev. 2010 Mar-Apr;29(2):197-246. doi: 10.1002/mas.20243. Mass Spectrom Rev. 2010. PMID: 19598206 Review.
-
Computational prediction of proteotypic peptides for quantitative proteomics.Nat Biotechnol. 2007 Jan;25(1):125-31. doi: 10.1038/nbt1275. Epub 2006 Dec 31. Nat Biotechnol. 2007. PMID: 17195840
Cited by
-
A tutorial for software development in quantitative proteomics using PSI standard formats.Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):88-97. doi: 10.1016/j.bbapap.2013.04.004. Epub 2013 Apr 12. Biochim Biophys Acta. 2014. PMID: 23584085 Free PMC article. Review.
-
mMass as a software tool for the annotation of cyclic peptide tandem mass spectra.PLoS One. 2012;7(9):e44913. doi: 10.1371/journal.pone.0044913. Epub 2012 Sep 13. PLoS One. 2012. PMID: 23028676 Free PMC article.
-
ProInfer: An interpretable protein inference tool leveraging on biological networks.PLoS Comput Biol. 2023 Mar 17;19(3):e1010961. doi: 10.1371/journal.pcbi.1010961. eCollection 2023 Mar. PLoS Comput Biol. 2023. PMID: 36930671 Free PMC article.
-
Software-aided detection and structural characterization of cyclic peptide metabolites in biological matrix by high-resolution mass spectrometry.J Pharm Anal. 2020 Jun;10(3):240-246. doi: 10.1016/j.jpha.2020.05.012. Epub 2020 May 26. J Pharm Anal. 2020. PMID: 32612870 Free PMC article.
-
Integration of proteomics, bioinformatics, and systems biology in traumatic brain injury biomarker discovery.Front Neurol. 2013 May 31;4:61. doi: 10.3389/fneur.2013.00061. eCollection 2013. Front Neurol. 2013. PMID: 23750150 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
