-
Notifications
You must be signed in to change notification settings - Fork 22
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Meaning of MS$FOCUSED_ION: ION_TYPE #176
Comments
Thank you for your report. You are right there are some inconsistencies with this tag. Actually I don't know how to treat MS$FOCUSED_ION: ION_TYPE and I can not exactly find out from historical records. We have two very similar tags MS$FOCUSED_ION: ION_TYPE where I don't know what it should be used for and MS$FOCUSED_ION: PRECURSOR_TYPE which is clearly the type of the precursor ion in MSn spectra. Its exactly used for this purpose in our records. I guess its a good idea to start a discussion about the meaning and usage of MS$FOCUSED_ION: ION_TYPE here. Any comments would be appreciated. |
And here are some numbers. We have:
12240 records with MS$FOCUSED_ION: ION_TYPE
6 records with MS$FOCUSED_ION: ION_TYPE & MS$FOCUSED_ION: PRECURSOR_TYPE A while ago e removed some MS$FOCUSED_ION: ION_TYPE from a number of record files if they had MS$FOCUSED_ION: ION_TYPE and MS$FOCUSED_ION: PRECURSOR_TYPE and both tags had the same ion and if they were MSn spectra. |
The documentation gives examples which may help you see the difference - there are likely very few records that make use of this (backed-up by your numbers): https://github.com/MassBank/MassBank-web/blob/master/Documentation/MassBankRecordFormat.md#251-subtag-precursor_type |
Currently tag 2.5.1 structure is: As my understanding, ION_TYPE is more appropriate for MS1 description. But in Tendem Mass Spectrometry, as show MS2 MS3, one ion type cannot describe multi precursor. Here, ION_TYPE is unsuitable. |
Agree that PRECURSOR_TYPE seems the more appropriate and it's the one used in RMassBank. Should we update the record specifications to indicate that PRECURSOR_TYPE is preferred? |
I completely checked 2.5.1 MS$FOCUSED_ION: ION_TYPE, found 3 ion type cannot pass the current validator:
[(M+NH3)+H]+ (NOT PASS) -->> [M+NH3+H]+ (PASS)
[(M+CH3COOH)-H]- (NOT PASS) -->> [M+CH3COOH-H]- (PASS)
It is mentioned in before. Just revise the Format Guide will fix this.
But I think [M+HCOO-]- is correct. Or [M+HCOOH-H]- ?
Anyway please pay attention to this problem.
The text was updated successfully, but these errors were encountered: