Using GFS to identify encoding genomic loci from protein mass spectral data

Current Protocols in Bioinformatics
Mark R Holmes, Morgan C Giddings

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.

References

Jan 1, 1981·Journal of Molecular Evolution·T F SmithW M Fitch
Oct 23, 2004·Science·UNKNOWN ENCODE Project Consortium

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