Msconvert Capabilities
From SPCTools
| Revision as of 18:58, 17 March 2010 Tfarrah (Talk | contribs) ← Previous diff |
Revision as of 18:59, 17 March 2010 Tfarrah (Talk | contribs) Next diff → |
||
| Line 17: | Line 17: | ||
| <h2>msconvert</h2> | <h2>msconvert</h2> | ||
| <h3>mzXML</h3> | <h3>mzXML</h3> | ||
| - | Conversion: produces truncated file | + | 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. |
| <br>X!Tandem search: | <br>X!Tandem search: | ||
| <br>TPP: | <br>TPP: | ||
| + | |||
| <h3>mzML</h3> | <h3>mzML</h3> | ||
| Conversion: OK | Conversion: OK | ||
Revision as of 18:59, 17 March 2010
Testing of MSconvert is in progress and results will be posted here as they come.
Msconvert can convert successfully to mzML. However, it does not work for mzXML fully. Trapper can convert to mzXML only.
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, produced no results. Omitting --convertWith flag, tried using massWolf, and failed.
X!Tandem search:
TPP:
msconvert
mzXML
Conversion:
X!Tandem search:
TPP:
mzML
Conversion:
X!Tandem search:
TPP:
MDS/Sciex for ABI and Agilent
Raw file type: .wiff file
raw-to-mzXML converter: mzWiff
mzWiff
mzXML
Conversion:
X!Tandem search:
TPP:
msconvert
mzXML
Conversion:
X!Tandem search:
TPP:
mzML
Conversion:
X!Tandem search:
TPP:
