Unit

UNIT 13.9 Using GFS to Identify Encoding Genomic Loci from Protein Mass Spectral Data

  1. Mark R. Holmes1,
  2. Morgan C. Giddings1,2,3

Published Online: 1 MAR 2008

DOI: 10.1002/0471250953.bi1309s21

Lab Protocol Title

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

Additional Information

How to Cite

Holmes, M. R. and Giddings, M. C. 2008. Using GFS to Identify Encoding Genomic Loci from Protein Mass Spectral Data. Current Protocols in Bioinformatics. 21:13.9:13.9.1–13.9.20.

Author Information

  1. 1

    Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina

  2. 2

    Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina

  3. 3

    Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina and North Carolina State University, Raleigh, North Carolina

Publication History

  1. Published Online: 1 MAR 2008
  2. Published Print: MAR 2008
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Abstract

Genome-based peptide fingerprint scanning (GFS) directly maps several types of protein mass spectral (MS) data to the loci in the genome that may have encoded for the protein. This process can be used either for protein identification or for proteogenomic mapping, which is gene-finding and annotation based on proteomic data. Inputs to the program are one or more mass spectrometry files from peptide mass fingerprinting and/or tandem MS (MS/MS) along with one or more sequences to search them against, and the output is the coordinates of any matches found. This unit describes the use of GFS and subsequent results analysis. Curr. Protoc. Bioinform. 21:13.9.1-13.9.20. © 2008 by John Wiley & Sons, Inc.

Keywords:

  • mass spectrometry;
  • protein identification;
  • proteogenomics
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