Msconvert Capabilities
From SPCTools
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:TPP Search failed
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, file converted, but not output files created or received. Zip file empty. Tried using ep server, new problem arose.
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:
