Re: [proteowizard-support] MSconvert crash with Waters data conversion

[Nick S. <nicksh@u.washington.edu>]

In the folder "220215PE7675-95-1_LockmassAdjusted.raw", all of the files
have become lowercase (e.g. "_func001.dat"). MsConvert decides that a .raw
folder contains Waters data by seeing if it contains any files whose names
start with "_FUNC", and the lowercase version of those filenames does not
get matched.
You might be able to fix things by changing the case of all of the
filenames so that they match what they were originally.
-- Nick


On Fri, Feb 25, 2022 at 12:06 PM Black, Brenna via proteowizard-support <
pro...@li...> wrote:

> Hi there,
>
>
>
> First off, thank you for creating such a wonderful conversion program as
> part of Proteowizard. We have used many times! Unfortunately, I am recently
> having a problem converting Waters .RAW files to .mzML format with
> MSconvert. MSconvert works wonderfully for the original files, but if I use
> MassLynx to first adjust for lockmass (we apply after data collection) and
> to centroid (automatic peak picking, after collection in profile),
> MSconvert crashes without an error notification when I try and convert
> these MassLynx adjusted files. I would prefer to use MassLynx to
> adjust/filter the data, as we have found this method best suited for the
> data collected on the Waters system. Have you encountered this before
> and/or are you able to give us some pointer on how to overcome is problem?
> An example file set can be downloaded from: here
> <https://www.dropbox.com/sh/gzo428p2zau3vxm/AAAiqoJpYCSXSbr1e7sy4ptma?dl=0>
>
>
>
> Thank you very much in advance!
>
> Best regards,
>
> Brenna Black, PhD
>
> Scientist
>
>
>
> National Renewable Energy Laboratory (NREL)
>
> 15013 Denver West Parkway | Golden, CO 80401
>
> Bre...@nr... | www.nrel.gov
>
>
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