Request for assistance (much thanks)

[grimace9527]

Hello Prof. Ivanov, It's me, Jim, again and this is a sincere request for assistance. Thank you very much. When using Biosaur2 to process a glycopeptide DDA MS data, there are some peptide (are identified by other software and the result is confident) features that can not be extracted. However, when using Dinosaur, they can be got. The Dinosaur and Biosaur processings did not depend on identification results. For example: The MS2 scan 5553 is identified as EEQFNSTYR (composition: C50H72N14O19) with a N-glycan modification Hex(4)HexNAc(4) (composition: C56H92N4O40), and the charge is 3+. We track the profile like this:

and the dinosaur result is like:

but the biosaur result is like:

It seems biosaur just skipped this area... I upload the result here and mzml on google (https://drive.google.com/file/d/16ofdkofQxYou7htLzSlQw3xGKv9FMl4S/view?usp=drive_link), and I wonder if anything about the parameter could be optimized to get this peptide feature? Or if there's other problem?

The parameters in dinosaur and biosaur2 are default.

Thanks again for your response!

Best wishes, Jim results.zip

[markmipt]

Hi Jim!

I've made a quick look of your data: The biosaur2 reports your feature with monoisotopic m/z = 879.0249 instead of 878.6872 which is reported by Dinosaur. Thus, biosaur2 assumes the first Isotope as monoisotopic peak which is wrong. The reason is mass shifts of isotopes. Theoretical m/z values for 0, 1, 2nd and 3rd isotopes are 878.6868, 879.02126, 879.3557 and 879.6901. However, the experimentally observed m/z values for isotopes are 878.687378 (-0.6 ppm), 879.024902 (-4.1 ppm), 879.360901 (-5.9 ppm), 879.695862 (-6.5 ppm). Probably, biosaur2 filter out real monoisotopic peak due to significant mass difference from expected isotopic peaks m/z values. I'll look into it in more details in a few days.

Regards, Mark

[grimace9527]

Hi Prof. Ivanov, Thanks a lot for your analysis. It's so kind of you to give assistance. As you mentioned, I think maybe I could try to modify the tolerance of isotopic peaks? I'll try other parameters and data files to find if it could work. And I'm willing to do something to make the Biosaur project better. If there's anything I can help, please tell me. It's my pleasure to keep in touch with you and learn from you and your works.

Best wishes, Jim

[grimace9527]

And I found an interesting result which may help: When I set the min and max mz in Biosaur2 settings to 878 and 880, the output result contains the feature which I want to get:

However when the settings are 350~1500 (default), this feature can not be got.

Here is the result using 878~880 as mz settings: HF_20211126_nanongp_1.features.biosaur.878to880.txt Hope this could help. Thanks again!