How to label the fragment type of NIST20?

[JosieHong]

Hi,

Thanks for the great work! When I tried to implement it on my server, I met some problems with splitting the data of 'HCD' and 'CID'.

Following the instructor in README, I exported lr_msms_nist and hr_msms_nist of NIST20. However, after parse_and_export.py, the fragment type (frag_mode) of them is NaN. So how do you label the fragment type of them?

Thanks,
Josie

[adamoyoung]

Hi Josie,

Sorry for the super (super) late reply, I somehow missed this issue.

When we processed the data, we only used spectra from the hr_nist_msms (high resolution) partition. I haven't tested the lr_nist_msms (low resolution) partition recently, so our preprocessing script might not work properly on those data.

However, looking at the lr_nist_msms.MSP file that I have, it seems to me like they do not include the "Frag_mode" metadata entries, which would explain your NaNs. Based on the context of this data, I think it's safe to assume they are all "CID". However, I do think there is a high degree of overlap between the low resolution and high resolution libraries, so I'm not sure how useful it will be to include these spectra in the training data.

[JosieHong]

I see. I will try hr_nist_msms first. Thanks a lot! ; )