I am also seeing this issue. The fix provided, adding <note type="input" label="protein, quick acetyl">no</note>, to the xml did not solve the problem.
Anyone have a fix that works for the Jackhammer version? -Joshua On Friday, February 20, 2015 at 1:53:46 PM UTC-5, zeyu sun wrote: > > 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:* [email protected] [mailto: >>> [email protected]] *On Behalf Of *GATTACA >>> *Sent:* Tuesday, May 14, 2013 11:42 AM >>> *To:* [email protected] >>> *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 [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. >>> >>> >>> >> -- 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. For more options, visit https://groups.google.com/d/optout.
