There are zero intensity peaks in the spectral library built by easypqp

[fcyu]

Hi Guo Ci @guoci ,

This is an issue from users. They find that some fragments in the spectral library have zero intensity. Could you please follow up and fix this?

Thanks,

Fengchao

[guoci]

Please provide data.

[fcyu]

I also don't have the specific data. You can start with the data you already have to see if there is this issue. I think you can also fix them by just checking the code.

[fcyu]

But let me try to contact the users to get the data first.

[haianhle]

@fcyu Fengchao, I don't have issue with zero intensity peaks, but I noticed that every precursor in spectral library (library.tsv) file has one with intensity 10000.0. What are these "library intensity"? Are these values normalized from 0 to 10000 among fragment ions for each precursor? I'm very new to proteomics so I apologize if I should have known this. Thank you so much. Anh

[anesvi]

Those are fragment ion intensities. The highest for each peptide is normalized to be 10000.

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@fcyuhttps://github.com/fcyu Fengchao, I don't have issue with zero intensity peaks, but I noticed that every precursor in spectral library (library.tsv) file has one with intensity 10000.0. What are these "library intensity"? Are these values normalized from 0 to 10000 among fragment ions for each precursor? I'm very new to proteomics so I apologize if I should have known this. Thank you so much. Anh

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