FluTyper-an algorithm for automated typing and subtyping of the influenza virus from high resolution mass spectral data

BackgroundHigh 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.ResultsA 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.ConclusionsFluTyper 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.

• Publication year

  2010

• Venue

  BMC Bioinformatics

• Publication date

  2010-05-19

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1186/1471-2105-11-266PMID 20482883PMCID 3098065
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Rapid Typing and Subtyping of Vaccine Strains of the Influenza Virus with High Resolution Mass Spectrometry

  2010cited by this paper
• Typing of human and animal strains of influenza virus with conserved signature peptides of matrix M1 protein by high resolution mass spectrometry.

  2010cited by this paper
• Subtyping of the influenza virus by high resolution mass spectrometry.

  2009influential reference
• The economic impact of pandemic influenza

  2009cited by this paper
• Signature peptides of influenza nucleoprotein for the typing and subtyping of the virus by high resolution mass spectrometry.

  2009cited by this paper
• Antigenicity of a Type A Influenza Virus Through Comparison of Hemagglutination Inhibition and Mass Spectrometry Immunoassays

  2009cited by this paper
• Antigenic and Genetic Characteristics of Swine-Origin 2009 A(H1N1) Influenza Viruses Circulating in Humans

  2009cited by this paper
• Mass spectrometry analysis of the influenza virus.

  2009cited by this paper
• Hemagglutination-inhibition test for avian influenza virus subtype identification and the detection and quantitation of serum antibodies to the avian influenza virus.

  2008cited by this paper
• Antigenic characterisation of H3N2 subtypes of the influenza virus by mass spectrometry.

  2007cited by this paper
• The Influenza Virus Resource at the National Center for Biotechnology Information

  2007cited by this paper
• Avian Influenza Virus (H5N1): a Threat to Human Health

  2007cited by this paper
• Fingerprinting a killer: surveillance of the influenza virus by mass spectrometry.

  2007cited by this paper
• A proteomics approach to survey the antigenicity of the influenza virus by mass spectrometry

  2006cited by this paper
• Examples of Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Developments: From Ion Physics to Remote Access Biochemical Mass Spectrometry

  2005cited by this paper
• Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus

  2002cited by this paper
• The geometry of shape space: application to influenza.

  2001cited by this paper
• Automated reduction and interpretation of

  2000cited by this paper
• Predicting the evolution of human influenza A.

  1999cited by this paper
• Antigenic surveillance of the influenza virus by mass spectrometry.

  1999cited by this paper
• Binding of RHOA G17V to p300 enhances its HAT activity: a new mechanism of epigenetic deregulation in TFH lymphoma

  1999cited by this paper
• Structural biology of viruses

  1997cited by this paper
• World Health Organization: A Fact Sheet

  1996cited by this paper
• Typing and subtyping of influenza viruses in clinical samples by PCR

  1995cited by this paper
• Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions

  1995influential reference
• A mathematical model for the European spread of influenza

  1994cited by this paper
• Statistical analysis of nucleotide sequences of the hemagglutinin gene of human influenza A viruses.

  1994cited by this paper
• CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

  1994cited by this paper
• High-resolution electrospray mass spectra of large molecules

  1991cited by this paper
• A mathematical model for the global spread of influenza

  1985cited by this paper
• THE WORLD HEALTH ORGANIZATION

  1954cited by this paper

• A Molecular Immunoproteomics Approach to Assess the Viral Antigenicity of Influenza.

  2019cites this paper
• Phylogenetic Analysis Using Protein Mass Spectrometry.

  2017cites this paper
• AfterQC: automatic filtering, trimming, error removing and quality control for fastq data

  2017cites this paper
• Subtyping of hepatitis C virus with high resolution mass spectrometry.

  2017cites this paper
• A multi prototype classification algorithm and its application to multi class diagnostics

  2015cites this paper
• FluClass: A novel algorithm and approach to score and visualize the phylogeny of the influenza virus using mass spectrometry.

  2015cites this paper
• Role of Analytics in Viral Safety

  2014cites this paper
• Evolution of influenza neuraminidase and the detection of antiviral resistant strains using mass trees.

  2014cites this paper
• Origins of the reassortant 2009 pandemic influenza virus through proteotyping with mass spectrometry.

  2014cites this paper
• Subtyping of influenza neuraminidase using mass spectrometry.

  2013cites this paper
• Incorporation of a Proteotyping Approach Using Mass Spectrometry for Surveillance of Influenza Virus in Cell-Cultured Strains

  2013cites this paper
• Bioinformatics of Human Proteomics

  2013cites this paper
• Proteotyping for the rapid identification of influenza virus and other biopathogens.

  2013cites this paper
• FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry

  2012cites this paper
• Processing of Mass Spectrometry Data in Clinical Applications

  2012cites this paper
• Improving influenza virus detection.

  2012cites this paper
• Mass spectrometric approaches to study enveloped viruses: New possibilities for structural biology and prophylactic medicine

  2012cites this paper
• Proteotyping to establish the lineage of type A H1N1 and type B human influenza virus.

  2011cites this paper
• Mass spectrometry based proteomic studies on viruses and hosts – A review

  2011cites this paper
• Evolution of H5N1 influenza virus through proteotyping of hemagglutinin with high resolution mass spectrometry.

  2011cites this paper