Systematic identification of single amino acid variants in glioma stem-cell-derived chromosome 19 proteins

J Proteome Res. 2015 Feb 6;14(2):778-86. doi: 10.1021/pr500810g. Epub 2014 Nov 25.


Novel proteoforms with single amino acid variations represent proteins that often have altered biological functions but are less explored in the human proteome. We have developed an approach, searching high quality shotgun proteomic data against an extended protein database, to identify expressed mutant proteoforms in glioma stem cell (GSC) lines. The systematic search of MS/MS spectra using PEAKS 7.0 as the search engine has recognized 17 chromosome 19 proteins in GSCs with altered amino acid sequences. The results were further verified by manual spectral examination, validating 19 proteoforms. One of the novel findings, a mutant form of branched-chain aminotransferase 2 (p.Thr186Arg), was verified at the transcript level and by targeted proteomics in several glioma stem cell lines. The structure of this proteoform was examined by molecular modeling in order to estimate conformational changes due to mutation that might lead to functional modifications potentially linked to glioma. Based on our initial findings, we believe that our approach presented could contribute to construct a more complete map of the human functional proteome.

Keywords: BCAT2 p.Thr186Arg; Chromosome-Centric Human Proteome Project; SRM assay; bioinformatics; cancer proteomics; chromosome 19; glioma stem cells; mass spectrometry; missense single nucleotide variants; single amino acid variants.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acids / chemistry*
  • Brain Neoplasms / chemistry*
  • Chromosomes, Human, Pair 19*
  • Glioma / chemistry*
  • Humans
  • Molecular Sequence Data
  • Neoplasm Proteins / chemistry*
  • Neoplastic Stem Cells / chemistry*
  • Transcriptome


  • Amino Acids
  • Neoplasm Proteins