Small question fragment_bin_tol

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Jan 11, 2024, 8:44:16 AMJan 11
to Comet ms/ms db search support

I just had a small question to double-check. I know we can consider the fragment_bin_tol as an ion fragment tolerance, i.e. 0.02 being somewhat similar as 0.02 Da tolerance. Now if I wanted to set this to an equivalent of 7 ppm, 10ppm , 15 ppm MS2 tolerance it would be best to specify as 0.007, 0.01 and 0.015 respectively?

I saw that the minimum value is 0.01 - this is still the case?

Thank you very much for the feedback,

Jimmy Eng

Feb 22, 2024, 5:21:38 PMFeb 22
to Comet ms/ms db search support
Sorry for the late response (as I didn't get notification of posts to this group since January).  With respect to your question, you can go smaller than 0.01 if you want but there's no point in trying to associate a PPM tolerance for Comet.  You can use 0.01 which in my testing years ago performs as well or even slightly better in some datasets than 0.02 but at the expense of twice the memory use for the spectral arrays.  It wasn't worth the trade-off for me hence why I suggest 0.02 for high-res ms/ms data.  But you can certainly use 0.01 or go smaller it's at the cost of more memory use ... you'll just have to run some tests with your data to see what's optimal for you in terms of identification performance (vs. memory use, search times, etc.).

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