Glycan files ready for Nathan

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Glycan files ready for Nathan #1252

Open kmartinez834 opened 4 weeks ago

kmartinez834 commented 4 weeks ago

All changes for 2.5 have been applied to https://github.com/glygener/glygen-glycan-pipeline. Please proceed with glycan export processing.

fyi @ubhuiyan

kmartinez834 commented 3 weeks ago

@edwardsnj I used your exact_synonym.txt file to map compositions to GlyTouCan accessions in the PDC file ccRCC_TMT_intact_glycopeptide_abundance_MD-MAD.tsv

Some of the comps were missing from exact_synonym.txt, but were present in the GNOme composition browser:

G84225JN,N2H11F1S0G0
G89045VA,N2H10F1S1G0
G54010QB,N4H8F1S0G0
G19918RR,N6H7F5S2G0
G38773MR,N6H3F4S2G0
G58908DB,N7H4F0S4G0
G06991MU,N10H12F1S1G0
G37995HC,N2H10F1S0G0
G94390IS,N7H8F4S0G0
G72197KC,N4H8F1S1G0
G57794FS,N8H10F0S3G0
G98129XB,N7H4F1S2G0
G68735SN,N4H7F1S2G0
G05119ZZ,N9H10F3S0G0
G15670WD,N5H6F1S5G0
G88313PD,N8H10F0S4G0
G42976ON,N9H11F0S3G0
G92551PG,N7H8F5S0G0
G45624GT,N12H5F2S3G0

And these I couldn't map from the file or the browser:

N6H7F4S4G0
N6H7F5S4G0
N8H10F6S1G0
N10H11F6S3G0

I'm attaching my file that maps all of the "Nglycan" strings to GlyTouCan accessions for reference: pdc_glytoucan_mapping.csv

edwardsnj commented 3 weeks ago

I already wrote code to do this mapping, the missing ones will need to be registered with GlyTouCan. The interactive GNOme browser does some normalization of the composition strings that helps it find compositions with zeros and monosaccharides in a different order.

edwardsnj commented 3 weeks ago

And I just added code to tolerate the "G" which you must have had to work around.

kmartinez834 commented 3 weeks ago

Got it. I created the mapping file for Robel to process the proteoform data, but wanted to make you aware of the issue.

Would you mind submitting the missing compositions to GlyTouCan? Not urgent this release, but when you get a chance.

edwardsnj commented 3 weeks ago

Submitted the missing compositions to GlyTouCan.

kmartinez834 commented 1 week ago

@edwardsnj are these accessions still pending?

edwardsnj commented 1 week ago

Here they are:

N6H7F4S4G0 HexNAc6Hex7Fuc4NeuAc4 G65344XH N6H7F4S4G0 HexNAc6Hex7Fuc4NeuAc5 G29580WD N8H10F6S1G0 HexNAc8Hex10Fuc6NeuAc1 G30521DU N10H11F6S3G0 HexNAc10Hex11Fuc6NeuAc3 G99660SU

kmartinez834 commented 1 week ago

Thanks a lot. Was Kiyoko able to help with that other topology structure you submitted for me?

edwardsnj commented 1 week ago

Yes (and no). Solution was to use another tool to generate corresponding WURCS sequence and submit that for registration. I haven't got back to it but I can make that happen today. Stay tuned.

edwardsnj commented 1 week ago

Here is the accession: G42752DG