tide-search low retained rates

[Jiali Yu]

Hi Crux developers, 

I was trying to run some old MS data someone else did in the lab with tide-search and got a really low number of retained peaks and too many out-of-range peaks. I suspected my colleague told me the wrong proteome but she confirmed that the species I used was correct. I looked at the ms1 and ms2 peaks are normal but I am not sure about it is the problem of MS data or the proteome database.

I attached the log file. Would you suggest rerunning the mass spec?

Thanks,

Jiali

[William Stafford Noble]

Hi Jiali,

The log file you shared is a bit odd, because it doesn't seem to contain the command line that you used (this would typically appear in the first few lines of the file). Did you remove it? Can you send the command line that you used?

My first suggestion would be to use param-medic to make sure you are using the right parameters for your data. But the out-of-range peaks are very strange, so I wonder if something else is going on. You might also consider using --spectrum-parser mstoolkit and see if that makes a difference.

Bill

[Jiali Yu]

Hi Bill,

Thank you for your suggestions, it was really helpful! I tried the param-medic and found my data has so few qualifying peaks (you can see it from the attached log file). We also looked at the raw peak files and found that it doesn't even have many ms2 peaks. We think the samples might not be of high quality and the whole experiment needs to be repeated. 

Thank you!

Jiali

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