List of 40 proteins as targets for pilot proteomics analysis of feed-switch samples (of liver, I presume).
E-mail from Simen Rød Sandve to Morten Skaugen 2015-08-11:
On Tue, Aug 11, 2015 at 10:01 AM, Simen Rød Sandve wrote: Please find attached an excel table with 40 proteins of interest (names, annotation, and protein sequence). I know we mentioned 20 proteins as a nice number to aim for in the targeted analyses – but we couldn't really seem to agree on a smaller subset . Please see if its possible to use all 40 in a 'targeted proteomics' run. If this cannot be done we can remove things from the list after you have identified 'unique' peptide sequences for each protein. Note that three of the protID identifiers in the list are not contained in the large fasta files with all annotated proteins that you used for the analyses.
MS replied: "One of the new sequences, CIGSSA_102625.t8, has zero unique peptides. Which is not surprising, since it is identical to CIGSSA_067031.t1." To which SRS answered: "Oopps – wasnt aware of that - you can exchange the CIGSSA_102625.t8 with CIGSSA_067031.t1. "
Column names and first row: gene expressed protein.detected gene.name select protID protSeq CIGSSA_084143 TRUE FALSE elovl1b TRUE CIGSSA_084143.t1 mlqdigdram...
Column definitions (to be verified by SRS): gene: Cigene-assigned identifier (CIG=Cigene, SSA=Salmo salar), now superseded by the NCBI identifiers for the salmon genome). Can still be looked up at http://salmobase.org/cgi-bin/gb2/gbrowse/salmon_GBrowse_Chr_NCBI/?name=CIGSSA_084143 expressed: ? protein.detected: ? gene.name: not a well-defined identifier, but can usually be looked up at http://identifiers.org/genecards. For instance, http://www.genecards.org/Search/Keyword?queryString=elovl1b leads to http://identifiers.org/genecards/elovl1 (publications often use ad-hoc suffices such as "b" after established gene names). select: TRUE if Simen wanted to select it for proteomics. protID: gene plus ".t1" suffix for transcript 1, etc. protSeq: amino acid sequence of protein
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