entab doesn't process Thermo RAW from Xcalibur 3.1

[talli]

Hello

I've used entab 0.3.1 on a RAW file generated by a Thermo LCMS using Xcalibur 3.1 but the data isn't getting processed. The file is opened and the columns are created but the values are not generated. I've included a link to the original files and attached the output CSV (github doesn't support uploading TSVs)

The command used to produce the file was:

entab -i angio_test.raw -p thermo_raw -o angio_test.tsv

Thanks!

PS

Thanks for making this wonderful software! It's changing our lab process entirely.

Thanks so much for making this wonderful library! It is changing our lab process entirely.

angio_test.csv

angio_test.raw

[bovee]

Thank you so much for the kind words and the example! The RAW support is still pretty rough. Right now it reads the "profile" file section for each MS scan, but I think your file may only have the "centroid" file section? Does that sound right/match up with your data collection parameters?

It should be possible (albeit a bit of work) to add in support for reading the centroids. I have some draft work for #30 (also trying to improve RAW support) that this would probably link into; my job has been pretty hectic lately, but hoping to get back into that draft and finish it over the next couple months.

[talli]

Hi Roderick

That's a good question. I've attached the output from ThermoRawFileParser that doesn't reference a "centroid" at all.

https://drive.google.com/drive/folders/114w6FJ5MTcIN--jecuJekijN6XeiEVzO?usp=sharing

Please allow me to do a bit more digging by asking the team that produced the data in the first place.

Thanks!

Talli