Gene annotation using peptide mass spectrometry

This webpage presents supplemental material relevant to the paper "Gene annotation using peptide mass spectrometry" (Stephen Tanner, Zhouxin Shen, Julio Ng, Liliana Florea, Roderic Guigó, Steven P. Briggs, and Vineet Bafna), to appear in Genome Research. Please visit our lab webpage to download our software or learn more about our research.

Our largest source of mass spectra was HEK293 cell culture. The mass spectra are available for download. (See here for a list of samples). In addition, several data-sets were downloaded from the PeptideAtlas repository. The samples analyzed were as follows:
  • A8_IP
  • HUPO12_run31
  • HUPO12_run32
  • HUPO12_run33
  • HUPO12_run34
  • HUPO22_M_CA_S
  • HUPO28_b1-CIT
  • HUPO28_b1-SERUM
  • HUPO28_b2-CIT
  • HUPO28_b2-SERUM
  • HUPO28_b3-CIT
  • HUPO28_b3-SERUM
  • HUPO28_Ref-CIT
  • HUPO28_Ref-SERUM
  • HUPO29_b1-CIT_1
  • HUPO29_b1-CIT_win1
  • HUPO29_b1-CIT_win2
  • HUPO29_b1-EDTA_1
  • HUPO29_b1-EDTA_win1
  • HUPO29_b1-EDTA_win2
  • HUPO29_b1-HEP
  • HUPO29_b1-SERUM
  • HUPO34
  • HUPO37_b1-HEP_2LCQ
  • HUPO40

    The annotation table for the genomic search contains all spectrum annotations which passed the p-value cutoff. Annotations were compared to the genomic locations of a corpus of known proteins (the "mapped proteins", as described in the paper) These annotations are assigned to the following categories:
  • Cat1 - Perfect match to a mapped exon
  • Cat2 - Contained in a known exon, but has mismatches. Often a coding SNP; occasionally an out-of-frame match.
  • Cat3 - A single-exon peptide not matching any known protein
  • Cat4 - Perfect match to a known protein, spanning an exon
  • Cat5 - Imperfect match to a known protein, spanning an exon. Often a coding SNP.
  • Cat6 - An intron-spanning peptide, one end of which hits a known exon.
  • Cat7 - An intron-spanning peptide, neither end of which hits a known exon.
    Click here to return to the supplemental data index, or here to visit our lab webpage.