TPP bug discovered!!!

[dre]

Hey guys,

I have been working with TPP for some time now and recently I noticed
the following bug. This is my workflow that results in the problem:

Thermo Orbitrap RAW file is inputted into tpp -> convert to mzxml ->
convert to mgf -> run mascot -> convert to pepXML

The problem is as follows:

When I use the mascot default modification Acetyl (protein N-term),
the TPP converter that converts the mascot output .DAT file to pepXML
format creates the following header in the pepXML file:

<aminoacid_modification aminoacid=" " mass="42.010559"
massdiff="42.010559" peptide_terminus="n" variable="Y"/>
<aminoacid_modification aminoacid="N" mass="156.053486"
massdiff="42.010559" peptide_terminus="n" variable="Y"/>
<aminoacid_modification aminoacid="-" mass="42.010559"
massdiff="42.010559" peptide_terminus="n" variable="Y"/>
<aminoacid_modification aminoacid="t" mass="42.010559"
massdiff="42.010559" peptide_terminus="n" variable="Y"/>
<aminoacid_modification aminoacid="e" mass="42.010559"
massdiff="42.010559" peptide_terminus="n" variable="Y"/>
<aminoacid_modification aminoacid="r" mass="42.010559"
massdiff="42.010559" peptide_terminus="n" variable="Y"/>
<aminoacid_modification aminoacid="m" mass="42.010559"
massdiff="42.010559" peptide_terminus="n" variable="Y"/>

If you look at this header closely, the entries are not only
meaningless, but there is something funny to be seen if you look at
the aminoacid="" entries:

aminoacid=" "
aminoacid="N"
aminoacid="-"
aminoacid="t" = N - term
aminoacid="e"
aminoacid="r"
aminoacid="m"

as far as I know the aminoacid property should indicate aminoacid
letters and not be spelling out N-term. This is obviously a parsing
error occurring somewhere during the conversion.


Regards,
Andrej

[Natalie Tasman]

Hello Andrej,

What version of the TPP are you working with, and on what system
(windows, linux, etc.)?

-Natalie

[dre]

Hey Natalie,

The version is TPP v4.2 JETSTREAM rev 0, Build 200902190939 and I run
on Windows XP

Andrej

[dre]

Any updates concerning this problem?