Hi, I want to follow up on this issue, Is there anyway to turn this default setting off? Although Nterm acetylation does add few more peptide hits, but it is useless when I try to do quantitation based on Nterm dimethylation, and it mess up with the ASAPratio calculation downstream. I have try to add <note type="input" label="protein, quick acetyl">no</note> to my parameter file, but it didn't work at all, the tandem still add acetylation to Nterm during the search. Also, can anyone tell me what does protein_terminus="N" exactly means here? N refers to "Nterm" of the protein? or N means "No", which means the acetylation happens in all peptide Nterm?
SunSun On Thursday, May 16, 2013 at 1:20:50 AM UTC+8, GATTACA wrote: > > 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:* spctools...@googlegroups.com [mailto:spctools...@googlegroups.com] >> *On Behalf Of *GATTACA >> *Sent:* Tuesday, May 14, 2013 11:42 AM >> *To:* spctools...@googlegroups.com >> *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> >> >> >> 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 spctools-discu...@googlegroups.com. >> To post to this group, send email to spctools...@googlegroups.com. >> 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
