More grist for the mill with respect to mzWiff, while I get a crash with the -c flag, if I used -c1 -c (MS and MS/MS centroiding), no crash.
With respect to other discussions, mzWiff outputs in cycle major order (all experiments of each cycle in order), as opposed to msconvert and the ABI tool. Furthermore, mzWiff's conversion time for my test case wiff/wiff.scan file (15 sample file of approximately 27K spectra, about 120Mb .wiff/ wiff.scan file, no peak detection) is about the same as for msconvert (about 10mins each) despite the cycle major order of output. - n On Jan 18, 10:46 am, Nathan Edwards <[email protected]> wrote: > 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 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
