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Sign upMeaning of MS$FOCUSED_ION: ION_TYPE #176
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Thank you for your report. You are right there are some inconsistencies with this tag. Actually I don't know how to treat MS$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$FOCUSED_ION: ION_TYPE here. Any comments would be appreciated. |
meier-rene
changed the title
Validator errors on ION_TYPE
Meaning of MS$FOCUSED_ION: ION_TYPE
May 14, 2019
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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. |
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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 |
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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. |
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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? |
zzjl20 commentedMay 14, 2019
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.