lipidxplorer issueshttps://gitlab.isas.de/lifs-public/lipidxplorer/-/issues2020-12-04T09:25:15Zhttps://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/26Have basic file check in import2020-12-04T09:25:15ZDominik SchwudkeHave basic file check in importReading of files and Averaging with result of ZERO MS-Peaks should raise an error message during import.
See example:
Importing: F:\LipidXplorer-1.2.8\191105_Geko\Chol_ES_Geko\190820_Batch190627_Chol_Best\190820_39265_a.mzML
> Nb. of M...Reading of files and Averaging with result of ZERO MS-Peaks should raise an error message during import.
See example:
Importing: F:\LipidXplorer-1.2.8\191105_Geko\Chol_ES_Geko\190820_Batch190627_Chol_Best\190820_39265_a.mzML
> Nb. of MS scans............... 18
> Nb. of MS peaks............... 215
> Nb. of MS/MS scans............ 36
> Nb. of MS/MS peaks............ 950
> Nb. of MS peaks (after avg.).. 0
> Spray stability:
> MaxTIC - MinTIC:............ 174.42% of median
That leads in the end to an error like this before alignment of sample:
> MS filter settings............ 0.60
> MS/MS filter settings......... 0.60
> Avg. Nb. of MS scans.......... 18
> Avg. Nb. of MS peaks.......... 25757
> Avg. Nb. of MS/MS scans....... 36
> Avg. Nb. of MS/MS peaks....... 7141
853.66 sec. for reading the spectra
0.00 sec. for calibrating the spectra
Aligning MS spectra linear
File "lx\gui\lpdxGUI.py", line 327, in run
File "lx\spectraImport.py", line 588, in doImport
File "lx\alignment.py", line 549, in mkSurveyLinear
File "lx\spectraContainer.py", line 1044, in checkOccupation
TypeError unsupported operand type(s) for *: 'float' and 'NoneType'LipidXplorer 1.2.9Eduardo MirandaEduardo Mirandahttps://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/24Check recalibration of spectra!2020-12-04T09:53:49ZDominik SchwudkeCheck recalibration of spectra!Hallo, in my Hands recalibration of spectra is not working anymore.
Please check from your side!Hallo, in my Hands recalibration of spectra is not working anymore.
Please check from your side!LipidXplorer 1.2.9Eduardo MirandaEduardo Mirandahttps://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/23Import time range2020-12-04T09:49:50ZDominik SchwudkeImport time rangeits not possible to handle float numbers correctly for 'timerange' in import. It is required for precise imports not based on scan filters.its not possible to handle float numbers correctly for 'timerange' in import. It is required for precise imports not based on scan filters.LipidXplorer 1.2.9Eduardo MirandaEduardo Mirandahttps://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/22Memory Handling / Clear Memory2020-12-04T09:45:34ZDominik SchwudkeMemory Handling / Clear Memorywith 1.2.8 we fill the RAM up fast. Unfortunately, every action by LX incrementally increase the blocked RAM. We should find a way that LX clears RAM after action.with 1.2.8 we fill the RAM up fast. Unfortunately, every action by LX incrementally increase the blocked RAM. We should find a way that LX clears RAM after action.LipidXplorer 1.2.9Eduardo MirandaEduardo Mirandahttps://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/21Add single file consisteny check during import2020-12-04T09:17:46ZDominik SchwudkeAdd single file consisteny check during importWhen files are loaded in prior implemment check for number of peaks in MS1 and MS2. Raise alert with naming of inconsisted file.
Number of MS1 peaks after alignment has to be > 0
If MS2 is imported
Number of MS2 scans > 0
Number of MS...When files are loaded in prior implemment check for number of peaks in MS1 and MS2. Raise alert with naming of inconsisted file.
Number of MS1 peaks after alignment has to be > 0
If MS2 is imported
Number of MS2 scans > 0
Number of MS2 peaks after alignment has to be > 0LipidXplorer 1.2.9Eduardo MirandaEduardo Mirandahttps://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/16LipidXplorer Tools Sum Composition to m/z is not implemented2020-12-04T12:50:13ZNils HoffmannLipidXplorer Tools Sum Composition to m/z is not implementedOn the 'MS Tools' pane, when I enter the tooltip: C39 H78 N O8 P and click on Sum-composition-to-m/z, nothing happens in the UI. There is output on the console:
`Traceback (most recent call last):
File "C:\Users\nils.hoffmann\PycharmP...On the 'MS Tools' pane, when I enter the tooltip: C39 H78 N O8 P and click on Sum-composition-to-m/z, nothing happens in the UI. There is output on the console:
`Traceback (most recent call last):
File "C:\Users\nils.hoffmann\PycharmProjects\gitlab.isas.de\lipidxplorer\lx\gui\lpdxGUI.py", line 4165, in OnSumCompositionToMass
outtext = "For %s:\nExact mass is %.6f; Double Bonds are: %.1f; charge is: %d" % (elemSeq, elemSeq.getWeight(), elemSeq.get_DB(), elemSeq.charge)
File "C:\Users\nils.hoffmann\PycharmProjects\gitlab.isas.de\lipidxplorer\lx\mfql\chemsc.py", line 462, in getWeight
self._weight += float(thing.get_weight())
File "C:\Users\nils.hoffmann\PycharmProjects\gitlab.isas.de\lipidxplorer\lx\mfql\chemsc.py", line 146, in get_weight
raise Exception("To be implemented...")
Exception: To be implemented...
Traceback (most recent call last):
File "C:\Users\nils.hoffmann\PycharmProjects\gitlab.isas.de\lipidxplorer\lx\gui\lpdxGUI.py", line 4165, in OnSumCompositionToMass
outtext = "For %s:\nExact mass is %.6f; Double Bonds are: %.1f; charge is: %d" % (elemSeq, elemSeq.getWeight(), elemSeq.get_DB(), elemSeq.charge)
File "C:\Users\nils.hoffmann\PycharmProjects\gitlab.isas.de\lipidxplorer\lx\mfql\chemsc.py", line 462, in getWeight
self._weight += float(thing.get_weight())
File "C:\Users\nils.hoffmann\PycharmProjects\gitlab.isas.de\lipidxplorer\lx\mfql\chemsc.py", line 146, in get_weight
raise Exception("To be implemented...")
Exception: To be implemented...`
The functionality is currently missing.
Update:
The functionality does not work, if one of the constraints is missing. The UI should give the user a clue, that it will not be able to calculate the m/z, if the constraints are not entered or invalid. Currently, there is only feedback if everything works out.LipidXplorer 1.2.9Eduardo MirandaEduardo Mirandahttps://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/5Mass assignements change absolute to relative scale.2020-12-04T08:49:40ZDominik SchwudkeMass assignements change absolute to relative scale.Mass assignments are working in absolute scale.
Always smalles value is taken for assignment of sum compositions.
Example:-10 ppm is preffered over 1ppm!Mass assignments are working in absolute scale.
Always smalles value is taken for assignment of sum compositions.
Example:-10 ppm is preffered over 1ppm!LipidXplorer 1.2.9Eduardo MirandaEduardo Miranda