Corrupted RAW files, how do you handle them?

[thanadol-git]

Hi,

Recently, I tried to analyse several RAW files from Thermo. It seems like there is no gold-standard way to check their quality that I could see. Do you have any suggestion or tip, maybe, to check the quality of the files (RAW or mzML) or pre-screen them before initiating the whole pipeline?

Thansk a lot!

Best,
Thanadol

[jpfeuffer]

Hi!

Very good question!
First of all, I would check the checksum of the file if you are downloading it and the hoster provides checksums.
Then I would use a python package that wraps the Thermo API (warning: ugly because you will need .NET or mono), e.g. alpharaw to do a full pass over the spectra, maybe extracting some basic information to see if it is corrupt.