Skip to content
Please note that GitHub no longer supports your web browser.

We recommend upgrading to the latest Google Chrome or Firefox.

Learn more

/MassBank-data

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

LC-QTOF-MS #103

Merged
merged 11 commits into from Nov 25, 2019
+6,532 −0

Conversation

@raalizadeh
Copy link

raalizadeh commented Nov 22, 2019

Bisphenol derivatives
raalizadeh added 2 commits Nov 22, 2019
@raalizadeh
LC-QTOF-MS
Loading status checks…
f140966 
Bisphenol derivatives
@raalizadeh
GC-APCI-QTOF
Loading status checks…
7cd18f4 
OCPs and PAHs
@tsufz
tsufz requested changes Nov 22, 2019
View changes
Copy link
Member

tsufz left a comment •
edited

@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

This comment has been minimized.

Sign in to view
Copy link
Collaborator

meier-rene commented Nov 22, 2019

@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

This comment has been minimized.

Sign in to view
Copy link
Author

raalizadeh commented Nov 22, 2019

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
raalizadeh added 2 commits Nov 22, 2019
@raalizadeh
GC-APCI-QTOF
0af82d9 
Changing the records
@raalizadeh
GC-APCI-QTOF
Loading status checks…
9030324 
OCPs and PAHs
@raalizadeh raalizadeh reopened this Nov 22, 2019
@raalizadeh raalizadeh requested a review from tsufz Nov 22, 2019
@tsufz
tsufz reviewed Nov 22, 2019
View changes
Copy link
Member

tsufz left a comment

@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?
raalizadeh added 2 commits Nov 23, 2019
@raalizadeh
LC-QTOF-MS
Loading status checks…
97ae8be 
MS/MS of Ammonium Adducts of Bisphenol A derivatives
@raalizadeh
LC-QTOF-MS
Loading status checks…
51513d1 
Bisphenol Duplicates Removed
@raalizadeh

This comment has been minimized.

Sign in to view
Copy link
Author

raalizadeh commented Nov 24, 2019

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?
raalizadeh added 2 commits Nov 24, 2019
@raalizadeh
GC-APCI-QTOF
Loading status checks…
32d8ef7 
space is removed from files name.
@raalizadeh
GC-APCI-QTOF
Loading status checks…
74feb50 
Publication tag is fixed.
@schymane

This comment has been minimized.

Sign in to view
Copy link
Member

schymane commented Nov 24, 2019

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
@schymane
schymane reviewed Nov 24, 2019
View changes
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:

This comment has been minimized.

Sign in to view
Copy link
@schymane

schymane Nov 24, 2019

Member

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)

This comment has been minimized.

Sign in to view
Copy link
@raalizadeh

raalizadeh Nov 24, 2019

Author

Hi there. All the files have ION_MODE tag, maybe the order is the problem (new format). Let me check, thanks.
@raalizadeh
GC-APCI-QTOF
Loading status checks…
7a1e1f0 
Removing publication tag and chaning the order of ion_mode tag.
@schymane

This comment has been minimized.

Sign in to view
Copy link
Member

schymane commented on 7a1e1f0 Nov 24, 2019

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

This comment has been minimized.

Sign in to view
Copy link
Author

raalizadeh commented Nov 24, 2019 •
edited

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

This comment has been minimized.

Sign in to view
Copy link
Member

schymane commented Nov 24, 2019

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
@raalizadeh
GC-APCI-QTOF
Loading status checks…
21c9683 
Stripping ":" from "FLOW_RATE" tag...
@schymane

This comment has been minimized.

Sign in to view
Copy link
Member

schymane commented Nov 24, 2019

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
@raalizadeh
GC-APCI-QTOF
Loading status checks…
e8a5d97 
Splash is fixed
@schymane schymane merged commit 1be5806 into MassBank:dev Nov 25, 2019
1 check passed
1 check passed
continuous-integration/travis-ci/pr The Travis CI build passed
Details
@schymane

This comment has been minimized.

Sign in to view
Copy link
Member

schymane commented Nov 25, 2019

Thanks for the contribution @raalizadeh - glad to see you could fix the SPLASH issue!
@raalizadeh

This comment has been minimized.

Sign in to view
Copy link
Author

raalizadeh commented Nov 25, 2019

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

This comment has been minimized.

Sign in to view
Copy link
Member

tsufz commented Nov 25, 2019

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

This comment has been minimized.

Sign in to view
Copy link
Member

schymane commented Nov 25, 2019

There is still one more outstanding pull request that someone (@tsufz ?) should look at before a release: #104
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@tsufz tsufz

@schymane schymane

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
4 participants
@raalizadeh @meier-rene @schymane @tsufz
You can’t perform that action at this time.