MiniWiki

Some Usage Notes

• Tolerance in Da (issue #54)

  • yes you can use both ppm and Da as tolerance units

• Use of EDC as Crosslinker (issue #42)

  • yes EDC and other negative mass crosslinker can be used
    • crosslinker:AsymetricSingleAminoAcidRestrictedCrossLinker:Name:EDC;MASS:-18.0105647;FIRSTLINKEDAMINOACIDS:E,D,cterm;SECONDLINKEDAMINOACIDS:K,S,Y,T,nterm

• site specific incorporation of amino acid analogues e.g. photo amino-acids Issue #42

  • xiSEARCH can handle these - best by defining them as modifications in the FASTA-file
  • Change the sequence in the FASTA XXXXXL(photo)XXX. This defines L with a variable modifcation of photo at this place only. Leaving out the brackets, like XXXXXLphotoXXX defines the modification as a fixed modification
  • to use as this as crosslinking point you need to define a crosslinker that reacts to Lphoto:
    • crosslinker:AsymetricSingleAminoAcidRestrictedCrossLinker:Name:diaz;MASS:-28.006148;FIRSTLINKEDAMINOACIDS:Lphoto;SECONDLINKEDAMINOACIDS:*

• terminal modifications (e.g. issue #48):

  • modification x with mass 123 on the protein n-terminal: modification:variable::SYMBOLEXT:x;MODIFIED:*;DELTAMASS:123;PROTEINPOSITION:nterm
    • independent of the terminal residue (MODIFIED:*) n-terminal peptides (PROTEINPOSITION:nterm) are searched with a variable modification of 123 on the n-terminal residue
  • modification x with mass 123 on the peptide n-terminal: modification:variable::SYMBOLEXT:x;MODIFIED:*;DELTAMASS:123;PEPTIDEPOSITION:nterm
    • independent of the terminal residue (MODIFIED:*) all peptide (PEPTIDEPOSITION:nterm) will are searched with a variable modification of 123
  • modification x with mass 123 on the peptide c-terminal if the c-terminal is a C: modification:variable::SYMBOLEXT:x;MODIFIED:C;DELTAMASS:123;PEPTIDEPOSITION:cterm
    • if the c-terminal residue is a C (MODIFIED:C) the peptide (PEPTIDEPOSITION:cterm) will be searched with a variable modification of 123