基于计算质谱的蛋白质组学入门。 - Suppr

Suppr

超能文献

Getting started in computational mass spectrometry-based proteomics.

作者信息

Vitek Olga

机构信息

Departments of Statistics and Computer Science, Purdue University, West Lafayette, Indiana, USA.

出版信息

PLoS Comput Biol. 2009 May;5(5):e1000366. doi: 10.1371/journal.pcbi.1000366. Epub 2009 May 29.

DOI:10.1371/journal.pcbi.1000366

PMID:19492072

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2668757/

Abstract

摘要

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d66a/2668757/f4ac58fa6876/pcbi.1000366.g001.jpg

相似文献

Getting started in computational mass spectrometry-based proteomics.

PLoS Comput Biol. 2009 May;5(5):e1000366. doi: 10.1371/journal.pcbi.1000366. Epub 2009 May 29.

Peptide sequence confidence in accurate mass and time analysis and its use in complex proteomics experiments.

J Proteome Res. 2008 Dec;7(12):5148-56. doi: 10.1021/pr8004502.

Protein identification using 2D-LC-MS/MS.

Methods. 2005 Mar;35(3):248-55. doi: 10.1016/j.ymeth.2004.08.016. Epub 2005 Jan 12.

Tagging life's ups and downs.

Trends Biotechnol. 2002 Nov;20(11):449. doi: 10.1016/s0167-7799(02)02066-8.

Improving mass and liquid chromatography based identification of proteins using bayesian scoring.

J Proteome Res. 2005 Nov-Dec;4(6):2174-84. doi: 10.1021/pr050251c.

Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments.

Bioinformatics. 2008 Jul 15;24(14):1590-5. doi: 10.1093/bioinformatics/btn240. Epub 2008 May 19.

Clinical proteomics: liquid chromatography-mass spectrometry purification systems.

Methods Mol Biol. 2011;681:473-83. doi: 10.1007/978-1-60761-913-0_28.

Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry.

Methods. 2010 Feb;50(2):77-84. doi: 10.1016/j.ymeth.2009.07.009. Epub 2009 Aug 3.

Data pre-processing in liquid chromatography-mass spectrometry-based proteomics.

Bioinformatics. 2005 Nov 1;21(21):4054-9. doi: 10.1093/bioinformatics/bti660. Epub 2005 Sep 8.

Offline and online liquid chromatography mass spectrometry in quantitative proteomics.

Comb Chem High Throughput Screen. 2009 Feb;12(2):185-93. doi: 10.2174/138620709787315418.

引用本文的文献

Detecting Significant Changes in Protein Abundance.

EuPA Open Proteom. 2015 Jun;7:11-19. doi: 10.1016/j.euprot.2015.02.002.

Pathway and network analysis in proteomics.

J Theor Biol. 2014 Dec 7;362:44-52. doi: 10.1016/j.jtbi.2014.05.031. Epub 2014 Jun 6.

Protein disulfide topology determination through the fusion of mass spectrometric analysis and sequence-based prediction using Dempster-Shafer theory.

BMC Bioinformatics. 2013;14 Suppl 2(Suppl 2):S20. doi: 10.1186/1471-2105-14-S2-S20. Epub 2013 Jan 21.

Context-sensitive markov models for peptide scoring and identification from tandem mass spectrometry.

OMICS. 2013 Feb;17(2):94-105. doi: 10.1089/omi.2012.0073. Epub 2013 Jan 5.

Statistical inference from multiple iTRAQ experiments without using common reference standards.

J Proteome Res. 2013 Feb 1;12(2):594-604. doi: 10.1021/pr300624g. Epub 2013 Jan 16.

Minireview: progress and challenges in proteomics data management, sharing, and integration.

Mol Endocrinol. 2012 Oct;26(10):1660-74. doi: 10.1210/me.2012-1180. Epub 2012 Aug 17.

iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates.

Mol Cell Proteomics. 2011 Dec;10(12):M111.007690. doi: 10.1074/mcp.M111.007690. Epub 2011 Aug 29.

A guided tour of the Trans-Proteomic Pipeline.

Proteomics. 2010 Mar;10(6):1150-9. doi: 10.1002/pmic.200900375.

本文引用的文献

Statistical design of quantitative mass spectrometry-based proteomic experiments.

J Proteome Res. 2009 May;8(5):2144-56. doi: 10.1021/pr8010099.

Breast cancer diagnosis from proteomic mass spectrometry data: a comparative evaluation.

Stat Appl Genet Mol Biol. 2008;7(2):Article15. doi: 10.2202/1544-6115.1435. Epub 2008 Dec 22.

Mass spectrometry based targeted protein quantification: methods and applications.

J Proteome Res. 2009 Feb;8(2):787-97. doi: 10.1021/pr800538n.

Building consensus spectral libraries for peptide identification in proteomics.

Nat Methods. 2008 Oct;5(10):873-5. doi: 10.1038/nmeth.1254. Epub 2008 Sep 21.

Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.

J Proteome Res. 2008 Nov;7(11):4878-89. doi: 10.1021/pr800484x. Epub 2008 Sep 13.

Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra.

Mol Cell Proteomics. 2009 Jan;8(1):53-69. doi: 10.1074/mcp.M800103-MCP200. Epub 2008 Aug 14.

Proteogenomics: needs and roles to be filled by proteomics in genome annotation.

Brief Funct Genomic Proteomic. 2008 Jan;7(1):50-62. doi: 10.1093/bfgp/eln010. Epub 2008 Mar 10.

Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics.

Physiol Genomics. 2008 Mar 14;33(1):18-25. doi: 10.1152/physiolgenomics.00298.2007. Epub 2008 Jan 22.

Gene-set approach for expression pattern analysis.

Brief Bioinform. 2008 May;9(3):189-97. doi: 10.1093/bib/bbn001. Epub 2008 Jan 17.

An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data.

J Proteome Res. 2008 Jan;7(1):51-61. doi: 10.1021/pr700758r. Epub 2008 Jan 4.

文献AI研究员

20分钟写一篇综述，助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型，支持多种主流文档格式。

立即体验

相似文献

Getting started in computational mass spectrometry-based proteomics.

PLoS Comput Biol. 2009 May;5(5):e1000366. doi: 10.1371/journal.pcbi.1000366. Epub 2009 May 29.

Peptide sequence confidence in accurate mass and time analysis and its use in complex proteomics experiments.

J Proteome Res. 2008 Dec;7(12):5148-56. doi: 10.1021/pr8004502.

Protein identification using 2D-LC-MS/MS.

Methods. 2005 Mar;35(3):248-55. doi: 10.1016/j.ymeth.2004.08.016. Epub 2005 Jan 12.

Tagging life's ups and downs.

Trends Biotechnol. 2002 Nov;20(11):449. doi: 10.1016/s0167-7799(02)02066-8.

Improving mass and liquid chromatography based identification of proteins using bayesian scoring.

J Proteome Res. 2005 Nov-Dec;4(6):2174-84. doi: 10.1021/pr050251c.

Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments.

Bioinformatics. 2008 Jul 15;24(14):1590-5. doi: 10.1093/bioinformatics/btn240. Epub 2008 May 19.

Clinical proteomics: liquid chromatography-mass spectrometry purification systems.

Methods Mol Biol. 2011;681:473-83. doi: 10.1007/978-1-60761-913-0_28.

Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry.

Methods. 2010 Feb;50(2):77-84. doi: 10.1016/j.ymeth.2009.07.009. Epub 2009 Aug 3.

Data pre-processing in liquid chromatography-mass spectrometry-based proteomics.

Bioinformatics. 2005 Nov 1;21(21):4054-9. doi: 10.1093/bioinformatics/bti660. Epub 2005 Sep 8.

Offline and online liquid chromatography mass spectrometry in quantitative proteomics.

Comb Chem High Throughput Screen. 2009 Feb;12(2):185-93. doi: 10.2174/138620709787315418.

引用本文的文献

Detecting Significant Changes in Protein Abundance.

EuPA Open Proteom. 2015 Jun;7:11-19. doi: 10.1016/j.euprot.2015.02.002.

Pathway and network analysis in proteomics.

J Theor Biol. 2014 Dec 7;362:44-52. doi: 10.1016/j.jtbi.2014.05.031. Epub 2014 Jun 6.

Protein disulfide topology determination through the fusion of mass spectrometric analysis and sequence-based prediction using Dempster-Shafer theory.

BMC Bioinformatics. 2013;14 Suppl 2(Suppl 2):S20. doi: 10.1186/1471-2105-14-S2-S20. Epub 2013 Jan 21.

Context-sensitive markov models for peptide scoring and identification from tandem mass spectrometry.

OMICS. 2013 Feb;17(2):94-105. doi: 10.1089/omi.2012.0073. Epub 2013 Jan 5.

Statistical inference from multiple iTRAQ experiments without using common reference standards.

J Proteome Res. 2013 Feb 1;12(2):594-604. doi: 10.1021/pr300624g. Epub 2013 Jan 16.

Minireview: progress and challenges in proteomics data management, sharing, and integration.

Mol Endocrinol. 2012 Oct;26(10):1660-74. doi: 10.1210/me.2012-1180. Epub 2012 Aug 17.

iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates.

Mol Cell Proteomics. 2011 Dec;10(12):M111.007690. doi: 10.1074/mcp.M111.007690. Epub 2011 Aug 29.

A guided tour of the Trans-Proteomic Pipeline.

Proteomics. 2010 Mar;10(6):1150-9. doi: 10.1002/pmic.200900375.

本文引用的文献

Statistical design of quantitative mass spectrometry-based proteomic experiments.

J Proteome Res. 2009 May;8(5):2144-56. doi: 10.1021/pr8010099.

Breast cancer diagnosis from proteomic mass spectrometry data: a comparative evaluation.

Stat Appl Genet Mol Biol. 2008;7(2):Article15. doi: 10.2202/1544-6115.1435. Epub 2008 Dec 22.

Mass spectrometry based targeted protein quantification: methods and applications.

J Proteome Res. 2009 Feb;8(2):787-97. doi: 10.1021/pr800538n.

Building consensus spectral libraries for peptide identification in proteomics.

Nat Methods. 2008 Oct;5(10):873-5. doi: 10.1038/nmeth.1254. Epub 2008 Sep 21.

Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.

J Proteome Res. 2008 Nov;7(11):4878-89. doi: 10.1021/pr800484x. Epub 2008 Sep 13.

Spectral dictionaries: Integrating de novo peptide sequencing with database search of tandem mass spectra.

Mol Cell Proteomics. 2009 Jan;8(1):53-69. doi: 10.1074/mcp.M800103-MCP200. Epub 2008 Aug 14.

Proteogenomics: needs and roles to be filled by proteomics in genome annotation.

Brief Funct Genomic Proteomic. 2008 Jan;7(1):50-62. doi: 10.1093/bfgp/eln010. Epub 2008 Mar 10.

Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics.

Physiol Genomics. 2008 Mar 14;33(1):18-25. doi: 10.1152/physiolgenomics.00298.2007. Epub 2008 Jan 22.

Gene-set approach for expression pattern analysis.

Brief Bioinform. 2008 May;9(3):189-97. doi: 10.1093/bib/bbn001. Epub 2008 Jan 17.

An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data.

J Proteome Res. 2008 Jan;7(1):51-61. doi: 10.1021/pr700758r. Epub 2008 Jan 4.