You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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.
==============================================================================
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-----
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...
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!
==============================================================================
13:41:20 NOTICE: Output file 'D:\extract\MSData-glyxtoolms-example\TOPPAS_out_8\TOPPAS_out\013-GenericWrapper-ETooloutFeature\Testprotein.featureXML' written.
==============================================================================
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
File "D:\extract\OpenMS-2.3.0\share/OpenMS/SCRIPTS/glyxFilter.py", line 407, in main
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...
==============================================================================
13:42:22 ERROR: GenericWrapper (glyxFilter) failed!
The text was updated successfully, but these errors were encountered: