A systematic model of the LC-MS proteomics pipeline
<p>Abstract</p> <p>Motivation</p> <p>Mass spectrometry is a complex technique used for large-scale protein profiling with clinical and pharmaceutical applications. While individual components in the system have been studied extensively, little work has been done to inte...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-10-01
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| Series: | BMC Genomics |
| _version_ | 1818215004850094080 |
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| author | Sun Youting Braga-Neto Ulisses Dougherty Edward R |
| author_facet | Sun Youting Braga-Neto Ulisses Dougherty Edward R |
| author_sort | Sun Youting |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Motivation</p> <p>Mass spectrometry is a complex technique used for large-scale protein profiling with clinical and pharmaceutical applications. While individual components in the system have been studied extensively, little work has been done to integrate various modules and evaluate them from a systems point of view.</p> <p>Results</p> <p>In this work, we investigate this problem by putting together the different modules in a typical proteomics work flow, in order to capture and analyze key factors that impact the number of identified peptides and quantified proteins, protein quantification error, differential expression results, and classification performance. The proposed proteomics pipeline model can be used to optimize the work flow as well as to pinpoint critical bottlenecks worth investing time and resources into for improving performance. Using the model-based approach proposed here, one can study systematically the critical problem of proteomic biomarker discovery, by means of simulation using ground-truthed synthetic MS data.</p> |
| first_indexed | 2024-12-12T06:29:11Z |
| format | Article |
| id | doaj.art-aa5430fc325842a69c1dc0af5cd5812c |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T06:29:11Z |
| publishDate | 2012-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-aa5430fc325842a69c1dc0af5cd5812c2022-12-22T00:34:40ZengBMCBMC Genomics1471-21642012-10-0113Suppl 6S210.1186/1471-2164-13-S6-S2A systematic model of the LC-MS proteomics pipelineSun YoutingBraga-Neto UlissesDougherty Edward R<p>Abstract</p> <p>Motivation</p> <p>Mass spectrometry is a complex technique used for large-scale protein profiling with clinical and pharmaceutical applications. While individual components in the system have been studied extensively, little work has been done to integrate various modules and evaluate them from a systems point of view.</p> <p>Results</p> <p>In this work, we investigate this problem by putting together the different modules in a typical proteomics work flow, in order to capture and analyze key factors that impact the number of identified peptides and quantified proteins, protein quantification error, differential expression results, and classification performance. The proposed proteomics pipeline model can be used to optimize the work flow as well as to pinpoint critical bottlenecks worth investing time and resources into for improving performance. Using the model-based approach proposed here, one can study systematically the critical problem of proteomic biomarker discovery, by means of simulation using ground-truthed synthetic MS data.</p> |
| spellingShingle | Sun Youting Braga-Neto Ulisses Dougherty Edward R A systematic model of the LC-MS proteomics pipeline BMC Genomics |
| title | A systematic model of the LC-MS proteomics pipeline |
| title_full | A systematic model of the LC-MS proteomics pipeline |
| title_fullStr | A systematic model of the LC-MS proteomics pipeline |
| title_full_unstemmed | A systematic model of the LC-MS proteomics pipeline |
| title_short | A systematic model of the LC-MS proteomics pipeline |
| title_sort | systematic model of the lc ms proteomics pipeline |
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