Computational methods for protein identification from mass spectrometry data.
Protein identification using mass spectrometry is an indispensable computational tool in the life sciences. A dramatic increase in the use of proteomic strategies to understand the biology of living systems generates an ongoing need for more effective, efficient, and accurate computational methods f...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2008-02-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0040012&type=printable |
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| author | Leo McHugh Jonathan W Arthur |
| author_facet | Leo McHugh Jonathan W Arthur |
| author_sort | Leo McHugh |
| collection | DOAJ |
| description | Protein identification using mass spectrometry is an indispensable computational tool in the life sciences. A dramatic increase in the use of proteomic strategies to understand the biology of living systems generates an ongoing need for more effective, efficient, and accurate computational methods for protein identification. A wide range of computational methods, each with various implementations, are available to complement different proteomic approaches. A solid knowledge of the range of algorithms available and, more critically, the accuracy and effectiveness of these techniques is essential to ensure as many of the proteins as possible, within any particular experiment, are correctly identified. Here, we undertake a systematic review of the currently available methods and algorithms for interpreting, managing, and analyzing biological data associated with protein identification. We summarize the advances in computational solutions as they have responded to corresponding advances in mass spectrometry hardware. The evolution of scoring algorithms and metrics for automated protein identification are also discussed with a focus on the relative performance of different techniques. We also consider the relative advantages and limitations of different techniques in particular biological contexts. Finally, we present our perspective on future developments in the area of computational protein identification by considering the most recent literature on new and promising approaches to the problem as well as identifying areas yet to be explored and the potential application of methods from other areas of computational biology. |
| format | Article |
| id | doaj-art-8ffed9761d7646308886cbfa76569adf |
| institution | DOAJ |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2008-02-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-8ffed9761d7646308886cbfa76569adf2025-08-20T03:16:18ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582008-02-0142e1210.1371/journal.pcbi.0040012Computational methods for protein identification from mass spectrometry data.Leo McHughJonathan W ArthurProtein identification using mass spectrometry is an indispensable computational tool in the life sciences. A dramatic increase in the use of proteomic strategies to understand the biology of living systems generates an ongoing need for more effective, efficient, and accurate computational methods for protein identification. A wide range of computational methods, each with various implementations, are available to complement different proteomic approaches. A solid knowledge of the range of algorithms available and, more critically, the accuracy and effectiveness of these techniques is essential to ensure as many of the proteins as possible, within any particular experiment, are correctly identified. Here, we undertake a systematic review of the currently available methods and algorithms for interpreting, managing, and analyzing biological data associated with protein identification. We summarize the advances in computational solutions as they have responded to corresponding advances in mass spectrometry hardware. The evolution of scoring algorithms and metrics for automated protein identification are also discussed with a focus on the relative performance of different techniques. We also consider the relative advantages and limitations of different techniques in particular biological contexts. Finally, we present our perspective on future developments in the area of computational protein identification by considering the most recent literature on new and promising approaches to the problem as well as identifying areas yet to be explored and the potential application of methods from other areas of computational biology.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0040012&type=printable |
| spellingShingle | Leo McHugh Jonathan W Arthur Computational methods for protein identification from mass spectrometry data. PLoS Computational Biology |
| title | Computational methods for protein identification from mass spectrometry data. |
| title_full | Computational methods for protein identification from mass spectrometry data. |
| title_fullStr | Computational methods for protein identification from mass spectrometry data. |
| title_full_unstemmed | Computational methods for protein identification from mass spectrometry data. |
| title_short | Computational methods for protein identification from mass spectrometry data. |
| title_sort | computational methods for protein identification from mass spectrometry data |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0040012&type=printable |
| work_keys_str_mv | AT leomchugh computationalmethodsforproteinidentificationfrommassspectrometrydata AT jonathanwarthur computationalmethodsforproteinidentificationfrommassspectrometrydata |