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Dev: RIKEN CSRS records #74

Merged
merged 6 commits into from Jun 14, 2019
Merged

Dev: RIKEN CSRS records #74

merged 6 commits into from Jun 14, 2019

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zzjl20
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@zzjl20 zzjl20 commented Jun 4, 2019

10239 records form RIKEN Center for Sustainable Resource Science

@zzjl20
Create PR300002.txt
d2c9ab2
@zzjl20
creat CSRS_RIKEN
f91bce3 
Center for Sustainable Resource Science, RIKEN
8655 records, prefix: PR3
@zzjl20
RIKEN CSRS update
eb6993c 
10239 records from Center for Sustainable Resource Science, RIKEN,
prefix: PR3
@zzjl20
fix forcused ion type
c1a1d2f 
[M+FA-H]- ->
[M+HCOO]-
@meier-rene
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Hi, I had a look in your contribution and could fix some issues myself. One of the points is the usage of MS$FOCUSED_ION: ION_TYPE. Recently we had a discussion about the usage of this tag in MassBank/MassBank-web#176 and came to the agreement, that it is better to use MS$FOCUSED_ION: PRECURSOR_TYPE for MS2 spectra. I changed this for all your records and I would appreciate it if you could change your code accordingly. Another point is the CH$FORMULA tag. If the measured molecule is already an ion than we expect something like [C42H69O12]-. Any chance to introduce this in your future contributions?

But there is another major thing I can not figure out: some spectra are positive mode and some are negative mode. But the adduct type is not in agreement with the ion mode.

I found 797 records with ION_MODE NEGATIVE and a positive adduct ion. example PR311184.txt
I found 4216 records with ION_MODE POSITIVE and a negative adduct ion. example PR308655.txt

Do you have any explanation for this?

@zzjl20
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zzjl20 commented Jun 5, 2019

Thank you for the help of MS$FOCUSED_ION: PRECURSOR_TYPE for MS2 fix. I made a note and will pay attention for my work.
For the CH$FORMULA, sorry I didn't notice the format changed on April 25th. I think I can solve this.
Ion_mode maybe is something wrong. I need to find out.

@zzjl20
revise PR3 records
137bedd 
1. replace: MS$FOCUSED_ION: ION_TYPE -> MS$FOCUSED_ION: PRECURSOR_TYPE
2.  revise formula into ionic format if MILES is ionic format
3. convert a mistake. Now ION_MODE NEGATIVE/POSITIVE is in agreement to adduct ion.
4. remove  some records, which the SMILES and formula are totally different. That must be a raw data mistake.
@meier-rene
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Thank you for your working on the data, it looks better now. Nevertheless the problem with the mismatch of ion mode and precursor type is not solved. I can see that you changed a lot of files but sometimes you changed it from 'correct' to 'incorrect' like in PR300001.txt. It was ION_MODE POSITIVE and PRECURSOR_TYPE [M+H]+ and now its ION_MODE NEGATIVE and PRECURSOR_TYPE [M+H]+.

I will attach a list with mismatches between ION_MODE and PRECURSOR_TYPE:
ionmode.txt

There are over 8000 records with this problem. Please correct them.

@zzjl20
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zzjl20 commented Jun 12, 2019

Feel frustrated...
OK, thank you for remind.
I will soon upload again.

@zzjl20
modify POS/NEG
839ec00 
modify 8655 records
@meier-rene meier-rene merged commit 23ccafa into MassBank:dev Jun 14, 2019
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Well done. Thank you for your contribution.

@zzjl20 zzjl20 deleted the dev branch June 16, 2019 01:29
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@zzjl20 @meier-rene