wiff2 creating two files yet only has one acquisition (suspected error source: special characters in acquisition name)

[flytortgua]

it seems that proteowizard is producing multiple files when only one is expected. with wiff2, it is expected that it produces multiple files depending on the number of acquisitions, however, it is is still producing multiple files even if the wiff2 file has one acquisition:

Here is an example of the issue we are facing:

Ea2_001_A_pos-Ea2_A4_1.wiff2 has nine different acquisitions(via Analyst or Explorer in Sciex OS): And these nine are properly converted by proteowizard here, having a separate mzXML per acquisition: However, both beePollen2_MQ_012.wiff2 and beePollen2_MQ_010.wiff2 have one acquisition as seen here: Yet they produce two distinct mzXML file:

lastly, we had another sample called BeesDeath_002.wiff2 This one was converted properly, and only produced a single mzXML file:

So we suppose the problem is related to the naming convention of the acquisition. however we aren't sure the root of the problem. we also contacted @Potriquet from Sciex about the issue.

Thanks

Mathieu Feraud

[chambm]

I suspect Analyst is hiding samples that are technically recorded, perhaps because they are corrupt or empty. Msconvert tries to convert all samples, and if it turns out to be corrupt it will leave an incomplete stub output file. If it turns out to be empty it will leave an empty output file (no spectra or chromatogram, just metadata). If you send me one of those WIFFs I can confirm.