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adamoyoung avatar adamoyoung commented on August 18, 2024

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.

from massformer.

JosieHong avatar JosieHong commented on August 18, 2024

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

from massformer.

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