FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data
<p>Abstract</p> <p>Background</p> <p>High resolution mass spectrometry has been employed to rapidly and accurately type and subtype influenza viruses. The detection of signature peptides with unique theoretical masses enables the unequivocal assignment of the type and s...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2010-05-01
|
| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/11/266 |
| _version_ | 1811297239160586240 |
|---|---|
| author | Schwahn Alexander B Wong Jason WH Downard Kevin M |
| author_facet | Schwahn Alexander B Wong Jason WH Downard Kevin M |
| author_sort | Schwahn Alexander B |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>High resolution mass spectrometry has been employed to rapidly and accurately type and subtype influenza viruses. The detection of signature peptides with unique theoretical masses enables the unequivocal assignment of the type and subtype of a given strain. This analysis has, to date, required the manual inspection of mass spectra of whole virus and antigen digests.</p> <p>Results</p> <p>A computer algorithm, FluTyper, has been designed and implemented to achieve the automated analysis of MALDI mass spectra recorded for proteolytic digests of the whole influenza virus and antigens. FluTyper incorporates the use of established signature peptides and newly developed naïve Bayes classifiers for four common influenza antigens, hemagglutinin, neuraminidase, nucleoprotein, and matrix protein 1, to type and subtype the influenza virus based on their detection within proteolytic peptide mass maps. Theoretical and experimental testing of the classifiers demonstrates their applicability at protein coverage rates normally achievable in mass mapping experiments. The application of FluTyper to whole virus and antigen digests of a range of different strains of the influenza virus is demonstrated.</p> <p>Conclusions</p> <p>FluTyper algorithm facilitates the rapid and automated typing and subtyping of the influenza virus from mass spectral data. The newly developed naïve Bayes classifiers increase the confidence of influenza virus subtyping, especially where signature peptides are not detected. FluTyper is expected to popularize the use of mass spectrometry to characterize influenza viruses.</p> |
| first_indexed | 2024-04-13T06:00:13Z |
| format | Article |
| id | doaj.art-2c1b64fffb84448da8945f28c6667943 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-04-13T06:00:13Z |
| publishDate | 2010-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-2c1b64fffb84448da8945f28c66679432022-12-22T02:59:27ZengBMCBMC Bioinformatics1471-21052010-05-0111126610.1186/1471-2105-11-266FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral dataSchwahn Alexander BWong Jason WHDownard Kevin M<p>Abstract</p> <p>Background</p> <p>High resolution mass spectrometry has been employed to rapidly and accurately type and subtype influenza viruses. The detection of signature peptides with unique theoretical masses enables the unequivocal assignment of the type and subtype of a given strain. This analysis has, to date, required the manual inspection of mass spectra of whole virus and antigen digests.</p> <p>Results</p> <p>A computer algorithm, FluTyper, has been designed and implemented to achieve the automated analysis of MALDI mass spectra recorded for proteolytic digests of the whole influenza virus and antigens. FluTyper incorporates the use of established signature peptides and newly developed naïve Bayes classifiers for four common influenza antigens, hemagglutinin, neuraminidase, nucleoprotein, and matrix protein 1, to type and subtype the influenza virus based on their detection within proteolytic peptide mass maps. Theoretical and experimental testing of the classifiers demonstrates their applicability at protein coverage rates normally achievable in mass mapping experiments. The application of FluTyper to whole virus and antigen digests of a range of different strains of the influenza virus is demonstrated.</p> <p>Conclusions</p> <p>FluTyper algorithm facilitates the rapid and automated typing and subtyping of the influenza virus from mass spectral data. The newly developed naïve Bayes classifiers increase the confidence of influenza virus subtyping, especially where signature peptides are not detected. FluTyper is expected to popularize the use of mass spectrometry to characterize influenza viruses.</p>http://www.biomedcentral.com/1471-2105/11/266 |
| spellingShingle | Schwahn Alexander B Wong Jason WH Downard Kevin M FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data BMC Bioinformatics |
| title | FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data |
| title_full | FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data |
| title_fullStr | FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data |
| title_full_unstemmed | FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data |
| title_short | FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data |
| title_sort | flutyper an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data |
| url | http://www.biomedcentral.com/1471-2105/11/266 |
| work_keys_str_mv | AT schwahnalexanderb flutyperanalgorithmforautomatedtypingandsubtypingoftheinfluenzavirusfromhighresolutionmassspectraldata AT wongjasonwh flutyperanalgorithmforautomatedtypingandsubtypingoftheinfluenzavirusfromhighresolutionmassspectraldata AT downardkevinm flutyperanalgorithmforautomatedtypingandsubtypingoftheinfluenzavirusfromhighresolutionmassspectraldata |