From SPCTools

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.

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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, produced no results. Omitting --convertWith flag, tried using massWolf, and failed. Second try managed to send file to server, took indefinitely long to convert and send back file--file has yet to have been received.
X!Tandem search:
TPP:

msconvert

mzXML

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

mzML

Conversion:
X!Tandem search:
TPP:

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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, 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: