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Description:
Open forum for discussing Seattle Proteome Center proteomics tools, asking questions, and suggesting new features.
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Agilent 6520 QTOF, search engine and mass tolerance differences
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All,
We have recently acquired an Agilent 6520 QTOF and are finding that
the performance of different search engines (with post-analysis by
PeptideProphet / ProteinProphet), and effects of using different
fragment mass tolerances are more complicated than for our other
instruments (Orbtrap / Bruker HCT / Waters QTOF / Bruker HCT / ABI... more »
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question about IProphet output
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dear list, i was wondering if someone could explain me why there are 2 interprophet result entries for each of the 'hit_rank=1' tags in the pep.xml generated by iprophet? cheers, andreas
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decoy detection
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Hi Everyone,
I am trying to detect false positive rates in my TPP runs. I want to
make sure that my probability result measures are actually correct. I
have read some papers describing high levels of false positives and
using decoy sets to correct for these errors.
I originally downloaded Mayu, made a fasta file with the appended... more »
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X!Tandem Output vs PepXML
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Hi,
I have recently converted an X!Tandem output file to PepXML format
using Tandem2XML utility. The X!Tandem output file was generated from
an MGF file. After the conversion, I compared the contents of the X!
Tandem output and PepXML files to try to determine which attributes in
the PepXML file represent related attributes in the X!Tandem output... more »
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CPFP - Pipeline based on TPP (Demo Server)
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Dear all,
A while ago (August I think), I posted r.e. our pipeline here at
Oxford, which is an alternative web front end to the TPP, and
automates submission of searches with Mascot/Tandem/OMSSA, followed by
TPP analysis including combination of search engine results with
iProphet. I've now been through the process of getting approval for... more »
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from mzML to mzXML
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I have an Applied Biosystems 4800 MALDI TOF TOF and I use an LC-MALDI
workflow. Applied Biosystems gave me a tool to convert all T2D files
from an LC-run in a mzML file. For every run I have one mzML
containing MS and MSMS information. The question is: Can I go back
from mzML to mzXML? The majority of software up to today uses mzXML... more »
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building on windows
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I'm building tpp on windows with VS8. I checked out 4.3. I have a
couple questions.
1. I wanted to check out the trunk but I could only find win_lib in
the branches; where is win_lib for the trunk?
2. I assume I need to extract some of the external libs but I can't
find anything in the readme files. In extern I found:... more »
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zero ions matched using X!Tandem + kscore on ETD data
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Hello All,
I'm using the latest stable release of TPP (4.3.1) to search some
phospho ETD data.
I've modified my tandem input file for ETD:
scoring, x ions: no
scoring, y ions: no
scoring, z ions: yes
scoring, a ions: no
scoring, b ions: no
scoring, c ions: yes
residue, potential modification mass: 15.994915@M,57@C... more »
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Importing Phenyx results
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Can anyone shed some light on how to get Phenyx results into the TPP?
I already have the pepxml output from Phenyx, but I imagine there is
some sort of conversion that needs to happen, as in its current state
the TPP doesnt seem to know what to do with it.
Thanks!
Chris
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protxml2html.pl IProphet XSL Fix
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All,
I've previously had problems getting iProphet .prot.xml to display
correctly when using xsltproc on Fedora Core 8 as the xslt processor.
Everything worked with Xalan but not xsltproc, and error messages
where confusing. I've now had a chance to debug the xsl, and the issue
is that an xsl:param tag is incorrectly positioned - it is not the... more »
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