X!Tandem/TPP adding modifications not specified

[GATTACA]

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

[Eric Deutsch]

Maybe you’re seeing this? This Tandem option is on by default:

 

http://www.thegpm.org/tandem/api/pqa.html

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[GATTACA]

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

[zeyu sun]

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

[Joshua Dunham]

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

[Eric Deutsch]

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”?

[zeyu sun]

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