From SPCTools

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

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Contents 1 Agilent 1.1 trapper 1.1.1 mzXML 1.2 msconvert 1.2.1 mzXML 1.2.2 mzML 2 Thermo 2.1 ReAdW 2.1.1 mzXML 2.2 msconvert 2.2.1 mzXML 2.2.2 mzML 3 Analyst 3.1 mzWiff 3.1.1 mzXML 3.2 msconvert 3.2.1 mzXML 3.2.2 mzML

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:

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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:search ran successfully, slight differences with the msconvert mzXML file
TPP:TPP Search successful

msconvert

mzXML

Conversion: Appears to be successful
X!Tandem search: Search completed, slight differences with the ReAdW converted mzXML file
TPP:Peptide prophet completed with warnings,protein prophet failed. Search completed

mzML

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

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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:started runtandemsearch but it didn't complete--once completed, zztandempostproccessing.log file was will of warnings
TPP:

mzML

Conversion:
X!Tandem search:
TPP: