http://groups.google.com/group/spctools-discuss Open forum for discussing Seattle Proteome Center proteomics tools, asking questions, and suggesting new features. 2009-12-23T04:23:30Z Google Groups Amit Yadav amit007thech...@gmail.com 2009-12-23T04:23:30Z http://groups.google.com/group/spctools-discuss/browse_thread/thread/2531f2d08966a240/670f6e1d89954fd6?show_docid=670f6e1d89954fd6

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

Zhi Sun z...@systemsbiology.org 2009-12-22T19:07:15Z http://groups.google.com/group/spctools-discuss/browse_thread/thread/2531f2d08966a240/fe4ba776b29db2cf?show_docid=fe4ba776b29db2cf

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

Zhi Sun z...@systemsbiology.org 2009-12-22T18:28:33Z http://groups.google.com/group/spctools-discuss/browse_thread/thread/71fc3fa30b25968e/51c5646dce326d18?show_docid=51c5646dce326d18

Hi All, <br> Have anyone ever specified several sets of residue modifications in the <br> tandem.params file to search silac data. The feature was added to X!tandem <br> in April 2009. It is described here. <br> <a target="_blank" rel=nofollow href="http://www.thegpm.org/tandem/api/rmm.html">[link]</a> <br> I ran X!tandem 2009.10.01 version and tried to use this feature. It only can

GATTACA dfer...@umich.edu 2009-12-22T16:12:38Z http://groups.google.com/group/spctools-discuss/browse_thread/thread/71fc3fa30b25968e/5ea8f54e9a6d3252?show_docid=5ea8f54e9a6d3252

No but it might help in debugging. You say TPP can't see the database <br> file in '/dbase/IPI/' which could mean that you store all your fasta <br> files in a directory called /dbase on a linux system. Alternatively, <br> this could be on a Windows system running cygwin. I couldn't tell <br> based on the error message.

Matthew Chambers matthew.chamb...@vanderbilt.edu 2009-12-22T15:58:19Z http://groups.google.com/group/spctools-discuss/browse_thread/thread/2531f2d08966a240/71bc2494419b988d?show_docid=71bc2494419b988d

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

hcadrexler hcadrex...@googlemail.com 2009-12-22T08:42:12Z http://groups.google.com/group/spctools-discuss/browse_thread/thread/71fc3fa30b25968e/75f4decaf09f3a4c?show_docid=75f4decaf09f3a4c

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

Amit Kumar Yadav amit007thech...@gmail.com 2009-12-22T04:26:52Z http://groups.google.com/group/spctools-discuss/browse_thread/thread/2531f2d08966a240/d9b98e77963114ec?show_docid=d9b98e77963114ec

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

Luis Mendoza lmend...@systemsbiology.org 2009-12-21T21:47:30Z http://groups.google.com/group/spctools-discuss/browse_thread/thread/09172534be0d55be/374f174484952266?show_docid=374f174484952266

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

Tomas tvai...@u.washington.edu 2009-12-21T21:19:59Z http://groups.google.com/group/spctools-discuss/browse_thread/thread/09172534be0d55be/479f9e6da99f07f8?show_docid=479f9e6da99f07f8

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

GATTACA dfer...@umich.edu 2009-12-21T15:53:28Z http://groups.google.com/group/spctools-discuss/browse_thread/thread/71fc3fa30b25968e/d191d74b1aaa9456?show_docid=d191d74b1aaa9456

What OS are you running? Windows? Linux?

hcadrexler hcadrex...@googlemail.com 2009-12-21T08:54:13Z http://groups.google.com/group/spctools-discuss/browse_thread/thread/71fc3fa30b25968e/e920e9b20f2ba6d1?show_docid=e920e9b20f2ba6d1

Hi everybody, <br> currently I am trying to work my way through TPP. Subsequent to <br> converting my Thermo .raw files to mzXML I tried to do a Sequest <br> search with these files, using a decoy database that I generated with <br> the TPP tool Decoy Database. Conversion seemed to work properly, <br> however, when I start the search I immediately get the error message

Mark Peedin peedi...@mc.duke.edu 2009-12-19T21:05:24Z http://groups.google.com/group/spctools-discuss/browse_thread/thread/bf4365fce3478d95/37092a035c775fa0?show_docid=37092a035c775fa0

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

rprambo robert_p_ra...@hotmail.com 2009-12-19T02:33:58Z http://groups.google.com/group/spctools-discuss/browse_thread/thread/611fd18c7a9599c5/a15cc2b8002283f3?show_docid=a15cc2b8002283f3

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

Mark Peedin peedi...@mc.duke.edu 2009-12-18T21:30:33Z http://groups.google.com/group/spctools-discuss/browse_thread/thread/bf4365fce3478d95/df1c14e83f4b44a4?show_docid=df1c14e83f4b44a4

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

Xuan Wang wangxuan1...@gmail.com 2009-12-18T02:02:17Z http://groups.google.com/group/spctools-discuss/browse_thread/thread/c564d7eec74d0c52/00ca1a89ee3efbfa?show_docid=00ca1a89ee3efbfa

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