I'm having a hard time figuring out how to convert .wiff files to any
of the open formats using any of the available tools.
1) mzWiff (4.3.1) w/ Analyst QS 2.0 installed:
Two issues I can identify at this time - the output file provided on
the command-line is ignored (output seems to go to new file that
encodes the sample number <basename>-s1.mzXML). More serious is the
error when using the -c (centroid) option (below).
------------------------------------------------------------------------------------------------------------------------
mzWiff.exe --mzXML -G -c -v "C:\TEMP\WiffFiles
\DC275_A_DC275_UF_25_min_1x_10ul.wiff" "C:\TEMP\WiffFiles
\DC275_A_DC275_UF_25_min_1x_10ul.mzXML"
Started: Tue Jan 18 10:25:26 2011
INFO: AnalystQS 2.0 (2000004) detected. Using v2.0 interface.
INFO: Analyst QS Version 2.0 is installed.
INFO: C:\TEMP\WiffFiles\DC275_A_DC275_UF_25_min_1x_10ul.wiff is
created with Ana
lyst QS 2.0
INFO: It has an associated scan file with extension .wiff.scan
INFO: Associated scan file located.
INFO: 1 sample(s) recorded.
INFO: Sample#1(DC275 UF 25 min 1x)
Started: Sample#1: Tue Jan 18 10:25:26 2011
INFO: Found Manufacturer tag "AB Sciex Instruments" in file.
INFO: Found Model tag "QSTAR Elite" in file.
INFO: Found Serial Number tag "AP010360604" in file.
INFO: Found Hardware Version tag "M401402 B4T0301 M3L1415 B3T0300" in
file.
INFO: Period#0, has 5 experiment(s) recorded.
INFO: Experiment#0: Scan(TOF MS1/+), 3357/3357
INFO: Experiment#1: Scan(TOF MS2/+), 208/3357
INFO: Experiment#2: Scan(TOF MS2/+), 32/3357
INFO: Experiment#3: Scan(TOF MS2/+), 10/3357
INFO: Experiment#4: Scan(TOF MS2/+), 2/3357
INFO: Allocated 3609 scan slot(s) via full sweep.
INFO: Using Precursor info from DDE data stream.
(got computer name: D6MSB7F1)
Calculating sha1-sum of C:\TEMP\WiffFiles
\DC275_A_DC275_UF_25_min_1x_10ul.wiff
--done (sha1):4955edf73daf7bb99fcfd8929d4ca0c381f2af78
.........100/3609
.........200/3609
.........300/3609
.........400/3609
.........500/3609
.........600/3609
.........700/3609
..
ERROR: COM error 80070057 while processing sample#1
INFO: error message: The parameter is incorrect.
Ended: Sample#1: Tue Jan 18 10:25:37 2011
Elapsed: Sample#1: 11 sec
Ended: Tue Jan 18 10:25:37 2011
Elapsed: 12 sec
------------------------------------------------------------------------------------------------------------------------
Without the -c option, the program completes without (obvious) issue.
2. msconvert (version below) w/ Skyline (0.7) installed.
ProteoWizard release: 2.1.2448 (2011-1-3)
ProteoWizard MSData: 2.1.2442 (2010-12-31)
ProteoWizard Analysis: 2.1.2442 (2010-12-31)
Build date: Jan 4 2011 12:56:29
C:\TEMP\WiffFiles>msconvert.exe -v
DC269_C_DC267_UF_20_25_min_5x_10ul.wiff
format: mzML (Precision_64 [ 1000514:Precision_64
1000515:Precision_32 ], ByteOrder_LittleEndian, Compression_None)
indexed="true"
outputPath: .
extension: .mzML
contactFilename:
filters:
filenames:
DC269_C_DC267_UF_20_25_min_5x_10ul.wiff
processing file: DC269_C_DC267_UF_20_25_min_5x_10ul.wiff
[msconvert.exe] Caught unknown exception.
3. ABI's Wiff to mzData Converter
Can't find this on the web anymore
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