Eric, Sorry for the later reply.....I actually switched to Comet workflow now... since I use dimethylation to do the labeling, and I search L and H labeled peptide separately as fixed modification, the tandem.pep.xml now have these two modifications in Nterm, <terminal_modification terminus="n" massdiff="28.03" mass="29.0378" protein_terminus="N" variable="Y"/> <terminal_modification terminus="n" massdiff="42.0106" mass="43.0184" protein_terminus="N" variable="Y" symbol="^" /><!--X! Tandem n-terminal AA variable modification--> The ASAPratio can not really tell which one is the label....
SunSun On Wednesday, May 27, 2015 at 1:01:37 AM UTC+8, Eric Deutsch wrote: > > I have no alternate suggestions, this should be the fix for Jackhammer and > any other version since 2010. I have never used the option myself as I have > not needed to. > > > > Can you explain in more detail why you want to turn them off? How does it > “mess > up with the ASAPratio calculation downstream”? > > > > > > > > *From:* Joshua Dunham [mailto:[email protected] <javascript:>] > *Sent:* Friday, May 22, 2015 12:20 PM > *To:* [email protected] <javascript:> > *Cc:* [email protected] <javascript:> > *Subject:* Re: [spctools-discuss] X!Tandem/TPP adding modifications not > specified > > > > 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.
