spctools-discuss Google Group

Re: [spctools-discuss] t2D converter

amit007thech...@gmail.com (Amit Yadav) — Wed, 23 Dec 2009 04:23:30 UT

Hi Zhi,
That would be so kind of you and of so much help. Please send it to me.And
thanks a lot in advance.

RE: [spctools-discuss] t2D converter

z...@systemsbiology.org (Zhi Sun) — Tue, 22 Dec 2009 19:07:15 UT

Hi Amit,
I have a script that run the ConvertPeakList through command line that
convert each t2d file into a mzXML file, get mslevel information from the
t2d file name, and then combine all the mzXML file into one big file. If you
want to have this, I can send it to you.
Zhi
-----Original Message-----

residue modification mass

z...@systemsbiology.org (Zhi Sun) — Tue, 22 Dec 2009 18:28:33 UT

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.
[link]
I ran X!tandem 2009.10.01 version and tried to use this feature. It only can

Re: database error message

dfer...@umich.edu (GATTACA) — Tue, 22 Dec 2009 16:12:38 UT

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.

Re: [spctools-discuss] t2D converter

matthew.chamb...@vanderbilt.edu (Matthew Chambers) — Tue, 22 Dec 2009 15:58:19 UT

If you have an install of GPS/Data Explorer, then PyMsXml (1st hit on
google) will convert for you. Otherwise, proteomecommons.org is the only
tool I know that will work.
-Matt

Re: database error message

hcadrex...@googlemail.com (hcadrexler) — Tue, 22 Dec 2009 08:42:12 UT

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

t2D converter

amit007thech...@gmail.com (Amit Kumar Yadav) — Tue, 22 Dec 2009 04:26:52 UT

Hi All,
Does anyone know of a .t2D to MzXML/PKL/DTA converter for t2D files
from ABI-MALDI TOF/TOF (4700/4800/5800)series MS instruments?
I know of one java utility from proteomecommons.org named
"ConvertPeakList.jnlp" but it seems to have many bugs. It doesnt
convert into PKL/DTA correctly but converts into txt files and mgf.

Re: [spctools-discuss] Re: protein group vs. subsumed entry

lmend...@systemsbiology.org (Luis Mendoza) — Mon, 21 Dec 2009 21:47:30 UT

Hello Tomas,
The latest version that we release is 4.3.1.; did you download the source
code from our Sourceforge page?
You may also want to either delete the old stylesheet (say, the
interact.prot.xsl file) or just choose to filter/sort the ProteinProphet
results to make use of the new code (e.g. choose to Sort by Probability).

Re: protein group vs. subsumed entry

tvai...@u.washington.edu (Tomas) — Mon, 21 Dec 2009 21:19:59 UT

Luis,
we have deployed on our Linux cluster TPP version 4.3.2, but with that
I see identical result to the one I described before.
Is there issue with the Linux version?
Tomas

Re: database error message

dfer...@umich.edu (GATTACA) — Mon, 21 Dec 2009 15:53:28 UT

What OS are you running? Windows? Linux?

database error message

hcadrex...@googlemail.com (hcadrexler) — Mon, 21 Dec 2009 08:54:13 UT

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

I will be out of the office from 12/21/2009 - 1/1/2010...

peedi...@mc.duke.edu (Mark Peedin) — Sat, 19 Dec 2009 21:05:24 UT

I will be out of the office starting 12/18/2009 and will not return until
01/04/2010.
Please feel free to leave a message, as I will be checking my email, from
time to time... Any action items, however, will have to wait until the 1st
week of Jan 2010...

PeptideProphet and Decoys

robert_p_ra...@hotmail.com (rprambo) — Sat, 19 Dec 2009 02:33:58 UT

Hi Everyone,
I am using X!Tandem as my search engine and would like to know WHEN
and HOW to include the decoy database? I used the TPP utility to
generate the decoy and concatenated that to my regular fasta database.
Do I start the search over with the combined database and then run
PeptideProphet with the box checked "Use decoy hits to pin down the

I will be out of the office from 12/21/2009 - 1/1/2010...

peedi...@mc.duke.edu (Mark Peedin) — Fri, 18 Dec 2009 21:30:33 UT

Re: [spctools-discuss] PeptideSieve

wangxuan1...@gmail.com (Xuan Wang) — Fri, 18 Dec 2009 02:02:17 UT

Thanks Luis! Is there any way I can find those flanking aminoacids?
2009/12/17 Luis Mendoza <lmend...@systemsbiology.org>