sirius-ms/sirius

Sirius 6 How do I know which Sirius internal ID corresponds to in the original ID in the input file?

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DY970313 commented

Hello,
I did a compound annotation task of mgf data using Sirius 6 with GUI. Everything was perfect until the results were exported.
But when I exported the summary file, I found that
1）.tsv files had no original ID, only Sirius ID.
For example: a feature in .mgf had an original ID of Unkown(0.09_396.0852m/z) and a Sirius ID of 589266962313865030, as shown below (in Sirius 6 GUI).
image
In all exported .tsv, there iwas no original ID. The exported IDs are as follows. .mgf and table derived from "FBMN export" were also all Sirius ID.

formulaId	alignedFeatureId	mappingFeatureId
589267320599701454	589266962313865030	589266962313865030

2）No report.mztab file was exported

So, I have no way of knowing which Sirius internal ID corresponds to in the original ID in the .mgf file, except in the GUI. However, I have thousands of features and cannot manually check them one by one on the GUI.
Is there any other way to get it?

Thank you very much！

DY970313 commented

As a supplement, I tried to replace the original ID by the simpler value, e.g. C1, C2 and C3. But the problem still existed.

MartinHoffmannJena commented

Hey,

are you able to share an example mgf containing compounds with an "original ID"?

DY970313 commented

Hey,

are you able to share an example mgf containing compounds with an "original ID"?

Of course, here's two features in my .mgf. The raw data (waters, .raw) was processed by Progenesis QI software and the fragments were exported as .msp file, and then converted to .mgf by MSP2MGF. Also, I tried to run the same .mgf on Sirius 5.7.8 and this issue did not occur.

BEGIN IONS
TITLE=Unknown (13.13_277.4333m/z)
CHARGE=1-
PEPMASS=277.4333
#Comment=13.13_277.4333m/z
99.9246 19.5822
233.2265 14.4502
259.2059 5.8892
265.1469 3.9191
269.2457 4.7878
275.2006 11.4235
277.2162 7155.4311
277.3005 48.1023
277.3527 102.2289
END IONS

BEGIN IONS
TITLE=Unknown (13.13_293.1783m/z)
CHARGE=1-
PEPMASS=293.1783
#Comment=13.13_293.1783m/z
99.9246 19.5822
233.2265 14.4502
259.2059 5.8892
265.1469 3.9191
269.2457 4.7878
275.2006 11.4235
277.2162 7155.4311
277.3005 48.1023
277.3527 102.2289
END IONS
MartinHoffmannJena commented

Hi,

The correct .mgf field for that is FEATURE_ID, not TITLE. The .mgf format is not really standardized, so everybody kind of uses different fields for different purposes. We use the TITLE field strictly as a name and grouping parameter, and the FEATURE_ID for the mapping.

For now, you could replace all your "TITLE" occurences with "FEATURE_ID", I'll check if TITLE and NAME are fields that we want to use as backup feature ids, if they are not defined

DY970313 commented

Hi,

The correct .mgf field for that is FEATURE_ID, not TITLE. The .mgf format is not really standardized, so everybody kind of uses different fields for different purposes. We use the TITLE field strictly as a name and grouping parameter, and the FEATURE_ID for the mapping.

For now, you could replace all your "TITLE" occurences with "FEATURE_ID", I'll check if TITLE and NAME are fields that we want to use as backup feature ids, if they are not defined

Thank you very much indeed!!!! My problem was solved perfectly!

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