Proteomics group

Category: Omics

Lead: Susumu Goto

Members: Susumu Goto, Yuki Moriya, Shin Kawano, Akiyasu C. Yoshizawa, Tsuyoshi Tabata, Yu Watanabe, Tomoyo Takami, Satoshi Tanaka, Masaki Murase

Analysis protocol

Human cell line data

Reference protein (peptide) database construction.

• Swiss-Prot database with all variations (1). -> Replace with UniProt?
• Human lung cancer cell line data (KERO): Create protein sequence data from KERO vcf and Ensembl (2).
  • Currently by AnnoVar -> probably better be replaced by VEP (in correspondence with TogoVar).
• Japanese and ExAC variation data (TogoVar): Create protein sequence data from TogoVar vcf and Ensembl by VEP (3).
• Merge 1 & 2 & 3.
• Create peptide sequence data using several cleavage enzymes: Trypsin, Trypsin/P, Lys-C, ...
  • Trypsin: [KR]|[^P], ([KR]|[KRIFL] sometimes not cleaved, but we do not consider this)
  • Trypsin/P: [KR]|*
  • Lys-C: [K]|*
  • Arg-N: *|[R]

Data structure:

Viewer Links to KERO / ChIP-Atlas?