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LC-QTOF-MS #103
LC-QTOF-MS #103
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Bisphenol derivatives
OCPs and PAHs
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@raalizadeh, GC-MS records are not according to the new Record Format. Please adjust them according to the settings for GC-MS in https://github.com/tsufz/MassBank-web/blob/update_record_format/Documentation/MassBankRecordFormat.md
Examples:
This is not a flow gradient, but a temperature gradient:
AC$CHROMATOGRAPHY: FLOW_GRADIENT 55 C (3 min);15 C/min-180(0 min);6.5 C/min-280(5 min);10 C/min-300(5.28 min)
The correct tag is:
AC$CHROMATOGRAPHY: COLUMN_TEMPERATURE_GRADIENT
Solvent: Helium is no solvent, the correct tag is:
AC$CHROMATOGRAPHY: CARRIER_GAS Helium
Correct AC$CHROMATOGRAPHY: FLOW_RATE 1.5 mL min-1
to
AC$CHROMATOGRAPHY: FLOW_RATE 1.5 mL/min
More information on the condition of the GC are also useful, check the draft new record format for details, please.
more easy to read version of the document can be found here. |
I will close this commit and add new files. I wrote some functions to modify the text files and adding some of these tags... |
Changing the records
OCPs and PAHs
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@meier-rene I don' t see an issue with the records. The travis log says that a file is missing or is it related to the new GC like tags?
MS/MS of Ammonium Adducts of Bisphenol A derivatives
Bisphenol Duplicates Removed
Hey guys, |
space is removed from files name.
Publication tag is fixed.
Hi @raalizadeh thanks for your contributions! I've just had a look at the travis report, I can't see the missing file error but it looks like ION_MODE is missing, can you check how this should be written and correct? e.g. |
Athens_Univ/AU590219.txt
Outdated
@@ -4,7 +4,7 @@ DATE: 2019.11.21 | |||
AUTHORS: Dimitrios E. Damalas, Stefanos Kokolakis, Reza Aalizadeh, Nikolaos Thomaidis, University of Athens | |||
LICENSE: CC BY | |||
COPYRIGHT: Copyright (C) 2019 Department of Chemistry, University of Athens | |||
PUBLICATION: |
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Regarding publication field ... if there is no publication, please remove this field rather than writing N/A. It is not a compulsory field (but possibly still comes through incorrectly in the settings in RMassBank)
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Hi there. All the files have ION_MODE tag, maybe the order is the problem (new format). Let me check, thanks.
Removing publication tag and chaning the order of ion_mode tag.
It seems like it has strict checkpoint and the "order of the tags" should be preserved. It now asks for SPLASH which is already there... but I think that SPLASH should come after chromatographic info... Any idea? |
Indeed the build fails again with errors and warnings but PK$SPLASH appears to be in the right place to me, also consistent with other records (top of PK$ section). @meier-rene any ideas what is going wrong here? Also @meier-rene @tsufz there are warnings re the use of the new fields .. can you confirm Reza is using these correctly and update the validator? |
Stripping ":" from "FLOW_RATE" tag...
Yes, now we have an interesting SPLASH bug - we are discussing by email. |
Splash is fixed
Thanks for the contribution @raalizadeh - glad to see you could fix the SPLASH issue! |
Thank you @schymane for the quick feedback... Yes, it is fixed (updated all the r packages...hehe) |
@meier-rene, hence, will there be a release now? If not, I will update from dev. |
Bisphenol derivatives