Corrupted raw files

[Adriana Domarques]

Hi dear, all Proteomics!!

My name is Adriana and recently I am trying to analyze a data set (64 raw files, ~1GB each raw file,  Lumos orbitrap Thermo) from G93A Sprague Dawley rat (ALS model) so, I have 2 groups (before and after symptoms), 4 biological replicates, and my samples were SDS page, each one was divided into 4 fractions and prior to the Maxquant run, I set up to include one PTM search as variable modification induced by reactive aldehyde HNE in His residues, (I include a match between runs, and LFQ). But completely fail at feature detection step, I try to find an answer to solve this problem in Maxquant group, and someone advise me to convert my raw files into mzXML format, but I fail again, in the description of this error says that :

"Index was outside the bounds of the array." So, I would like to know if someone could help me to understand what is this error mean, and more importantly, I will feel extraordinary grateful if someone has a suggestion to solve this problem because I conducted by my own all steps of this experiment (especially for the lives from my rats, that spent about 3 months to developed ALS symptoms), and I trying to save all huge work that I had. 

Best regards, Adriana.

[Brian Pratt]

If you are using msconvert for the mzXML conversion, you should ask your question on the ProteoWizard support board by emailing sup...@proteowizard.org.

Best,

Brian Pratt

--
You received this message because you are subscribed to the Google Groups "ProteomicsQA" group.
To unsubscribe from this group and stop receiving emails from it, send an email to proteomicsqa...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/proteomicsqa/028f3860-e316-4ed8-854a-44a49a27458a%40googlegroups.com.

[dtabb1973]

Hi, Adriana.

I have routinely used this ProteoWizard msConvert line to produce mzML files for later ID in MSFragger, MS-GF+, or MyriMatch.

msconvert.exe --filter "peakPicking true 1-" -z *.raw

I have only rarely tried MaxQuant, and I seem to have an unusual knack for encountering errors in that software.

If you have a wide variety of potential modifications to consider, you might want to try MSFragger open search.  We found that very useful for FFPE: https://doi.org/10.1016/j.ijms.2019.116266

Good luck!
Dave