Hi Gautam,
This is because a single WIFF can contain multiple "samples", each of which translate to a separate
mzML document. Each document can't be named the same, so we append the "sample name", or if that's
not unique, we add a duplicate count like "(2)". An override was recently added to msconvert for
setting the output filename, but I expect that would explode for a multi-sample WIFF file (which are
not at all uncommon).
-Matt
On 1/19/2012 8:41 AM, Gautam Saxena wrote:
Hi,
When using msconvert on ABI wiff files, it seems to suffix the
converted output file with the word "-Sample". Is this intended? This
suffixing does not occurr with Thermo .raw files, so why should it
occur with wiff files? Here's an example output:
===========================
R:\programs\windows_programs\msconvert\msconvert.exe --filter "msLevel
2-" --mzXML --64 --mz64 --inten32 F:/JHU_NHLBI_MS_FILES/
Melanies_iTRAQ_data/wiff_files/Fraction1/Fr1_1.wiff
format: mzXML (Precision_64 [ 1000514:Precision_64
1000515:Precision_32 ], ByteOrder_LittleEndian, Compression_None)
indexed="true"
outputPath: .
extension: .mzXML
contactFilename:
filters:
msLevel 2-
filenames:
F:/JHU_NHLBI_MS_FILES/Melanies_iTRAQ_data/wiff_files/Fraction1/
Fr1_1.wiff
processing file: F:/JHU_NHLBI_MS_FILES/Melanies_iTRAQ_data/wiff_files/
Fraction1/Fr1_1.wiff
writing output file: ./Fr1_1-Sample.mzXML
=========================
The version of msconvert being used is shown below:
==========================================
W:\lab1\jsmith_university_edu\Workflow_Outputs\DJ8C>R:\programs
\windows_programs\msconvert\msconvert.exe --version
unknown option version
Please report this error to [email protected].
Attach the command output and this version information in your report:
ProteoWizard release: 2.2.2997 (2011-9-19)
ProteoWizard MSData: 2.2.2997 (2011-9-19)
ProteoWizard Analysis: 2.2.2976 (2011-9-14)
Build date: Sep 19 2011 17:00:29
===========================================
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