Failure to execute glyxFilter (own data)

[a-g-007]

Hi Markus,

I have been playing around with your tools to see whether they might help me with my glycopeptide analysis. So far, I've been able to run both sample workflows, but when I tried to adjust the Fibrinogen workflow to my own analysis, the glyxFilter node fails to execute. Everything until that point seems to work well. The data was measured on a Waters Xevo G2-S qTOF instrument with CID fragmentation. The protein contains a single O-glycosylation and no N-glycosylation site. The glycosylated peptide was fragment and can be found in the .featurexml file.

There are several errors in the output of that node (copied below), but I guess what causes it to break down is the division by zero. I checked the .featureXML file and I could not find ions that were listed as containing zero charge. I also tried several different node settings but nothing seemed to fix it.

Best regards,
Andreas

13:41:20 NOTICE: GenericWrapper (FeatureFinderMS) finished!

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13:41:20 NOTICE: Output file 'D:\extract\MSData-glyxtoolms-example\TOPPAS_out_8\TOPPAS_out\013-GenericWrapper-ETooloutFeature\Testprotein.featureXML' written.

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13:41:20 NOTICE: GenericWrapper (glyxFilter) of node #11 started. Processing ...
Startig glyxFilter
GenericWrapper took 01:01 m (wall), 0.00 s (CPU), 0.00 s (system), 0.00 s (user).
External tool returned with exit code (1), exit status (0) or timed out. Aborting ...
External tool output:
------oxoniumIonList-----

(HexNAc)1(H2O)-1(H+)1 {'charge': 1, 'mass': 186.07611, 'depends': ['(HexNAc)1(H+)1']}

(Hex)2(HexNAc)1(NeuAc)1(H+)1 {'charge': 1, 'mass': 819.2876799999999, 'depends': ['(NeuAc)1(H+)1']}

(Hex)1(HexNAc)1(NeuAc)2(H+)1 {'charge': 1, 'mass': 948.33028, 'depends': ['(NeuAc)1(H+)1']}

(HexNAc)1(Hex)2(H+)1 {'charge': 1, 'mass': 528.19228}

(Hex)1(H+)1 {'charge': 1, 'mass': 163.06008, 'depends': ['(Hex)1(H2O)-1(H+)1']}

(HexNAc)1(H+)1 {'charge': 1, 'mass': 204.08668, 'depends': ['(HexNAc)1(H2O)-1(H+)1']}

(Hex)1(H2O)-1(H+)1 {'charge': 1, 'mass': 145.04951, 'depends': ['(Hex)1(H+)1']}

(HexNAc)1(Hex)1(H+)1 {'charge': 1, 'mass': 366.13948}

(NeuAc)1(H2O)-1(H+)1 {'charge': 1, 'mass': 274.09211, 'depends': ['(NeuAc)1(H+)1']}

(NeuAc)1(H+)1 {'charge': 1, 'mass': 292.10267999999996, 'depends': ['(NeuAc)1(H2O)-1(H+)1']}

(Hex)1(HexNAc)1(NeuAc)1(H+)1 {'charge': 1, 'mass': 657.23488, 'depends': ['(NeuAc)1(H+)1']}

loading feature file

loading experiment

While loading 'C:\Users\Andi\AppData\Local\Temp\20181005_131215_8048_1\testprotein\008_GenericWrapper_FileBuilder\EToolout\Testprotein.mzML': Name of CV term not correct: 'MS:1000422 - high-energy collision-induced dissociation' should be 'beam-type collision-induced dissociation'

loading finnished

skipped 0 single charged spectra

writing outputfile

Traceback (most recent call last):

File "D:\extract\OpenMS-2.3.0\share/OpenMS/SCRIPTS/glyxFilter.py", line 485, in

main(handle_args())

File "D:\extract\OpenMS-2.3.0\share/OpenMS/SCRIPTS/glyxFilter.py", line 407, in main

maxMZ = minMZ+1/float(score.precursorCharge)*3 # TODO: handle other Adducts

ZeroDivisionError: float division by zero

<While loading 'C:\Users\Andi\AppData\Local\Temp\20181005_131215_8048_1\testprotein\008_GenericWrapper_FileBuilder\EToolout\Testprotein.mzML': Name of CV term not correct: 'MS:1000422 - high-energy collision-induced dissociation' should be 'beam-type collision-induced dissociation'> occurred 896 times

This is printed in case of error - you can list possible causes for failure here...

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13:42:22 ERROR: GenericWrapper (glyxFilter) failed!