Thanks Eric! That did it. I would never have found this one. Damian
On Tuesday, May 14, 2013 2:49:22 PM UTC-4, Eric Deutsch wrote: > > Maybe you’re seeing this? This Tandem option is on by default: > > > > http://www.thegpm.org/tandem/api/pqa.html > > > > > > > > *From:* [email protected] <javascript:> [mailto: > [email protected] <javascript:>] *On Behalf Of *GATTACA > *Sent:* Tuesday, May 14, 2013 11:42 AM > *To:* [email protected] <javascript:> > *Subject:* [spctools-discuss] X!Tandem/TPP adding modifications not > specified > > > > 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"> > 15.9...@M,80@S,80@T,80@Y</note <javascript:>> > > > 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] <javascript:>. > To post to this group, send email to [email protected]<javascript:> > . > Visit this group at http://groups.google.com/group/spctools-discuss?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- 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.
