Hello Alex,
Glad that you were able to get to the bottom of this issue and hope you
have been able to process your data.
I just wanted to add that when installing TPP on Windows, the entire
ProteoWizard set of tools (including msConvert GUI) is also bundled -- so
there is typically no need to
Dear David,
So after a long troubleshooting process with msConvert and Waters team as
well as testing it by myself, I found the best way to convert Waters.raw
files is to use this Waters proprietary software
https://microapps.on-demand.waters.com/home/showmarkdown/data-as-a-product to
Hello Alex,
This is pointing to a bug in either the Waters library for access to the raw
data or in msconvert. Perhaps you can contact Waters and msconvert developers
to see if they have patched the problem. My suspicion as to the nature of the
problem is use of signed (as opposed to
Hi David,
I do not know why. The data was acquired on MassLynx by a Waters Xevo QTOF
set to fast DDA, with scan times of MS1 and MS2 set to both 1s with 10 MS2
scans. The lockspray mass is also included. The settings, besides the scan
times, were not changed from the last time I ran the data,
Hello Alex,
I was able to download your file, convert the data to mzML using msconvert and
read a few spectra using the command line tool readMzXml (works on mzML too).
Unfortunately, I am finding many intensities these files that are encoded with
negative values, which is likely causing
Hi David,
Thank you for your prompt feedback! The file can be found at the link
below.
https://drive.google.com/file/d/1QulcwZ3UP7pcMtECNwubd4DysqaDq4UN/view?usp=sharing
Looking forward to your inputs!
Best,
Alex
On Friday, January 5, 2024 at 1:09:03 AM UTC+1 David Shteynberg wrote:
>
Hello Alex,
Thanks for trying the TPP pipeline to solve your proteomics computational
needs. Sorry, you are having trouble converting and analyzing Waters raw data.
Have you tried using the latest version of msconvert to do the conversion to
mzML? If you are able to upload your file to an
Hi guys,
So I've used TPP before to convert bottom up proteomic Thermo raw files in
msconvert, comet search with custom params file, and xinteract to perform
protein prophet with no issues. Earlier this year, I performed the same
with Waters. Raw file, although in the beginning there was an
