When running msconvert (latest stable release: 2.2.3214 , which we
downloaded today) on a wiff file, we got the following error:

Error writing run 1 in Fr1_3.wiff:
[ExperimentImpl::getBPC] Index was outside the bounds of the array.

(We did not get this error on 40 other wiff files.) The way in which
we called this msconvert was as follows:

R:\programs\windows_programs\msconvert\msconvert.exe --filter "msLevel
2-" --mzXML --64 --mz64 --inten32 M:/XXXXX/iTRAQ_data/wiff_files/
Fraction1/Fr1_3.wiff

Any clues?

What's strange, as well, though is that we think (though we're not
100% sure) that msconvert still retunred a "success" code -- as in,
the msconvert program returned a code of 0, implying that it
succeeded, when it clearly did not. (The mzXML file never got
created.)

More details:

ProteoWizard release: 2.2.3214 (2012-1-13)
ProteoWizard MSData: 2.2.3214 (2012-1-13)
ProteoWizard Analysis: 2.2.3214 (2012-1-13)
Build date: Jan 17 2012 15:54:29

-Gautam

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