Msconvert Capabilities

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Conversion: using remoteconvert.pl --convertWith readw, file successfully converted. Conversion: using remoteconvert.pl --convertWith readw, file successfully converted.
<br>X!Tandem search: <br>X!Tandem search:
-<br>TPP:+<br>TPP:TPP Search successful
<h2>msconvert</h2> <h2>msconvert</h2>

Revision as of 23:38, 31 March 2010

Testing of MSconvert is in progress and results will be posted here as they come.

Contents

Agilent

Raw file type: .d directory
raw-to-mzXML converter: trapper

trapper

mzXML

Conversion: OK
X!Tandem search: OK
TPP: PeptideProphet results were all probability=0. Why? WEIRD.

msconvert

mzXML

Conversion: produces truncated file. Zhi says that msconvert is not able to convert MRM data to mzXML format. So we don't expect this to work.
X!Tandem search:
TPP:

mzML

Conversion: OK
X!Tandem search: Terry had to edit runtandemsearch to make it work on mzML. Then, search ran for 7 days without completing. Zhi thinks she has seen the same problem.
TPP:


Thermo

Raw file type: .RAW file
raw-to-mzXML converter: ReAdW

ReAdW

mzXML

Conversion: using remoteconvert.pl --convertWith readw, file successfully converted.
X!Tandem search:
TPP:TPP Search successful

msconvert

mzXML

Conversion: Appears to be successful
X!Tandem search: Search completed
TPP:Peptide prophet completed with warnings,protein prophet failed.

mzML

Conversion: Conversion seemed to work. TPP tests did not work with mzML file format
X!Tandem search:
TPP:


Analyst

Raw file type: .wiff file
raw-to-mzXML converter: mzWiff

mzWiff

mzXML

Conversion: used /regis/sbeams/bin/remoteconvert.pl --default --convertWith mzWiff QS20061230_P0094_C1_08_AQv1.1.wiff, waited 5 minutes but nothing happened.
X!Tandem search:
TPP:

msconvert

mzXML

Conversion:Tried /regis/sbeams/bin/remoteconvert.pl --default --convertWith msconvert QS20061230_P0094_C1_08_AQv1.1.wiff, could not connect with server. Also tried /regis/sbeams/bin/remoteconvert.pl --default --server th --convertWith msconvert QS20061230_P0094_C1_08_AQv1.1.wiff, also could not connect to server. Tried using both actual file and symbolic link for .wiff file; same problem as above.
X!Tandem search:
TPP:

mzML

Conversion:
X!Tandem search:
TPP:

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