database error message

[hcadrexler]

Hi everybody,

currently I am trying to work my way through TPP. Subsequent to
converting my Thermo .raw files to mzXML I tried to do a Sequest
search with these files, using a decoy database that I generated with
the TPP tool Decoy Database. Conversion seemed to work properly,
however, when I start the search I immediately get the error message
"Cannot read the database file '/dbase/IPI/
ipi.MOUSE.v3.64_DECOY.fasta'. Check that this filename is correct.".
The file name appears to be correct, the file is located where it is
supposed to be, the database is specified in the params file, yet....
Does anybody have a clue on what might have gone wrong?

[GATTACA]

What OS are you running? Windows? Linux?

[hcadrexler]

I am running Windows XP 32-bit - would it make a difference?

[GATTACA]

No but it might help in debugging. You say TPP can't see the database
file in '/dbase/IPI/' which could mean that you store all your fasta
files in a directory called /dbase on a linux system. Alternatively,
this could be on a Windows system running cygwin. I couldn't tell
based on the error message.
I think Sequest file paths on Windows should look like this: C:\dbase
\IPI\ipi.MOUSE.v3.64_DECOY.fasta
NOT like what you posted: '/dbase/IPI/ipi.MOUSE.v3.64_DECOY.fasta'

Get the full path to your fasta file using Windows Explorer and use
that path in Sequest.

HTH,
GATTACA

[Zhi Sun]

Hi All,

Have anyone ever specified several sets of residue modifications in the
tandem.params file to search silac data. The feature was added to X!tandem
in April 2009. It is described here.
http://www.thegpm.org/tandem/api/rmm.html

I ran X!tandem 2009.10.01 version and tried to use this feature. It only can
find the first modification I specified in the parameter file. I post part
of my parameter setting blow. Is there anything I did wrong?

****************************************************************************
<note type="input" label="residue, modification mass">57.021464@C</note>
<note type="input" label="residue, modification mass 1">4.0@K,6.0@R</note>
<note type="input" label="residue, modification mass 2">8.0@K,10.0@R</note>

<note type="input" label="refine, potential modification
mass">15.994915@M</note>
<note type="input" label="refine, potential modification
motif">0.984016@N!{P}[ST]{P}</note>
<note type="input" label="refine">yes</note>
***************************************************************************

Also, for the third residue modification, should I put the difference of the
mass between third one and the second one or not?

Thanks a lot,
Zhi

[Hannes Drexler]

Hi HTH,
you may be right - I will have a closer look at the path. Thanks for
your help! Happy Holidays!

Hannes

2009/12/22 GATTACA <dfe...@umich.edu>:

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