This is a weird one: X!Tandem/TPP seems to be inserting n-terminal acetylation modifications to searches without being told to do so.
Since updating our pipeline to TPP 4.6.2 we are occasionally seeing n-terminal acetylation (+42@[) in our results. For instance, the input.xml file contains: <note type="input" label="residue, modification mass">57@C</note> <note type="input" label="residue, potential modification mass">15.994915@M,80@S,80@T,80@Y</note> Looking at the output of Tandem2XML I see that it detects the modifications shown above, but it also detects +42@[ <terminal_modification terminus="n" massdiff="42.0106" mass="43.0184" protein_terminus="N" variable="Y" symbol="^" /><!--X! Tandem n-terminal AA variable modification--> We never specified the n-terminal modification. The raw X!Tandem XML output does *NOT* indicate that this modification was provided. So where is it coming from? It appears to occur randomly. It has been observed in different samples from different labs. When it does happen, the file sizes for the search results are significantly inflated (ie: file sizes are > 40MB when usually are in the range of 8-10MB). I've looked at the default_input.xml files used by X!Tandem and the +42@[ isn't given there. Any suggestions? Thanks -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
