ms files in dataset Deep_29_healthy_human_tissues_PXD010154

[sophiachen1]

Hi @wenbostar,

I have a quick question about dataset Deep_29_healthy_human_tissues_PXD010154, I saw in PRIDE this dataset contains about 1800 ms raw files https://www.ebi.ac.uk/pride/archive/projects/PXD010154 , while I checked the supplementary data 1 of pepquery2 paper that the n_ms_file is 1474 for this cohort. Is there any prefiltering on MS raw data before collecting them into pepquery2 database?

Thank you so much for your help!
Sophia

[wenbostar]

Yes. Attahced please find the list of raw files used in the paper.

PXD010154_index_summary.txt

[sophiachen1]

Thanks for your quick response @wenbostar ! Do you have an idea about how long it takes to index all raw data in this list? and how much memory it requires for the task?

[wenbostar]

After you download the raw files and convert them to mzML files, the indexing should not take long: probably one or two hours. It doesn't require large memory: one or two G ram should be enough.