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LC-QTOF-MS #103

Merged
merged 11 commits into from Nov 25, 2019
Merged

LC-QTOF-MS #103

merged 11 commits into from Nov 25, 2019

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raalizadeh
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Bisphenol derivatives

Bisphenol derivatives
OCPs and PAHs
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@tsufz tsufz left a comment

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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.

@meier-rene
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@raalizadeh

https://github.com/tsufz/MassBank-web/blob/update_record_format/Documentation/MassBankRecordFormat.md

more easy to read version of the document can be found here.

@raalizadeh
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I will close this commit and add new files. I wrote some functions to modify the text files and adding some of these tags...
Sorry for the inconvenience, I did not notice that we have got new template for the MassBank record.

@raalizadeh raalizadeh closed this Nov 22, 2019
Changing the records
OCPs and PAHs
@raalizadeh raalizadeh reopened this Nov 22, 2019
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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
@raalizadeh
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Hey guys,
I fixed the LC-ESI-QTOF and GC-APCI-QTOF data, but whenever I create pull request, as Tobias said above, it keeps saying that a file is missing. Any idea what causes it?

space is removed from files name.
Publication tag is fixed.
@schymane
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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.
https://travis-ci.org/MassBank/MassBank-data/jobs/616223930#L2663

@@ -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.
@raalizadeh
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raalizadeh commented Nov 24, 2019

Thanks Reza! Let's wait and see what Travis says ..

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?

@schymane
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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?
e.g.
https://travis-ci.org/MassBank/MassBank-data/jobs/616239382#L2418
vs
7a1e1f0#diff-1f3a027e953f969d159efd4b4dce961aL45
image

image

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?
The warnings and errors start here:
https://travis-ci.org/MassBank/MassBank-data/jobs/616239382#L2415

Stripping ":" from "FLOW_RATE" tag...
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Yes, now we have an interesting SPLASH bug - we are discussing by email.
https://travis-ci.org/MassBank/MassBank-data/jobs/616251567#L2418
For some reason one block is missing, which does not make sense according to latest RMB:
https://github.com/MassBank/RMassBank/blob/master/R/getSplash.R

Splash is fixed
@schymane schymane merged commit 1be5806 into MassBank:dev Nov 25, 2019
@schymane
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Thanks for the contribution @raalizadeh - glad to see you could fix the SPLASH issue!

@raalizadeh
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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)

@tsufz
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tsufz commented Nov 25, 2019

@meier-rene, hence, will there be a release now? If not, I will update from dev.

@schymane
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There is still one more outstanding pull request that someone (@tsufz ?) should look at before a release: #104

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4 participants