lipidxplorer issueshttps://gitlab.isas.de/lifs-public/lipidxplorer/-/issues2020-12-04T12:50:13Zhttps://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/4Ask user for consent before overwriting out file, master scan, dump files etc.2020-12-04T12:03:06ZNils HoffmannAsk user for consent before overwriting out file, master scan, dump files etc.LipidXplorer 1.2.9https://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/7Remove DDA support in import / spectra classes2020-12-04T09:57:06ZNils HoffmannRemove DDA support in import / spectra classesMoved here from issue #2Moved here from issue #2LipidXplorer 1.2.9https://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/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/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/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 Mirandahttps://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/25Interface Import Settings "configuration Save AS" does not work2019-12-12T07:12:30ZDominik SchwudkeInterface Import Settings "configuration Save AS" does not workI can not save an import configuration using "Save As" option.I can not save an import configuration using "Save As" option.LipidXplorer 1.2.8.1Nils HoffmannNils Hoffmannhttps://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/10Add benchmark data2019-10-13T10:02:26ZDominik SchwudkeAdd benchmark dataPlease add the benchmark data for relaese of 1.2.8
Also results have to be added.Please add the benchmark data for relaese of 1.2.8
Also results have to be added.LipidXplorer 1.2.8https://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/11Default Import settings have to be defined2019-10-13T10:01:58ZDominik SchwudkeDefault Import settings have to be definedImport settings Default has to be defined. For first time open the software *.ini file does not exist.
Settings should be defined from benchmark.Import settings Default has to be defined. For first time open the software *.ini file does not exist.
Settings should be defined from benchmark.LipidXplorer 1.2.8https://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/17Please check MS Tools pane for working and missing functionality2019-10-13T10:01:27ZNils HoffmannPlease check MS Tools pane for working and missing functionalityIn order to prepare release 1.2.8, please check that all functionality on the 'MS Tools' pane is actually working and documented in the Wiki.
Whatever is not working at the moment, should be either fixed, if that seems reasonable to do, ...In order to prepare release 1.2.8, please check that all functionality on the 'MS Tools' pane is actually working and documented in the Wiki.
Whatever is not working at the moment, should be either fixed, if that seems reasonable to do, or it should be disabled for now.LipidXplorer 1.2.8Eduardo MirandaEduardo Mirandahttps://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/18Releasework LipidXplorer 1.2.82019-10-13T10:00:59ZNils HoffmannReleasework LipidXplorer 1.2.8* [x] Update https://bio.tools/lipidxplorer
* [x] Fix MPI Wiki to guide to new Wiki at https://lifs.isas.de/wiki
* [x] Bundle / zip benchmark data
* [x] Upload release material to lifs portal
* [x] Write release note on lifs portal
...* [x] Update https://bio.tools/lipidxplorer
* [x] Fix MPI Wiki to guide to new Wiki at https://lifs.isas.de/wiki
* [x] Bundle / zip benchmark data
* [x] Upload release material to lifs portal
* [x] Write release note on lifs portal
* [x] Create a zenodo releaseLipidXplorer 1.2.8Nils HoffmannNils Hoffmann2019-10-11https://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/13WIKI - entrie on resoultion needs to be corrected2019-10-01T12:21:38ZDominik SchwudkeWIKI - entrie on resoultion needs to be corrected"resolution: the resolution of the mass spectrometer in MS and MS/MS mode.
This value is used in the import for the spectra averaging and alignment. Both algorithms consider m/z values as equal if they are closer than the resolution all..."resolution: the resolution of the mass spectrometer in MS and MS/MS mode.
This value is used in the import for the spectra averaging and alignment. Both algorithms consider m/z values as equal if they are closer than the resolution allows."
**Add:**
Value given here defines resolution at the smallest m/z value of a give m/z range. Resolution will be computed according to slope given in "resolution gradient".LipidXplorer 1.2.8Eduardo MirandaEduardo Mirandahttps://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/12WIKI for Import - Add frequency filter explaination2019-09-13T10:58:11ZDominik SchwudkeWIKI for Import - Add frequency filter explainationLipidXplorer 1.2.8Dr. Fadi Al MachotDr. Fadi Al Machothttps://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/2Remove DDA / DTA support2019-09-11T09:51:46ZNils HoffmannRemove DDA / DTA supportThe DDA CSV support in LipidXplorer seems to be obsolete. It should be removed.
* [x] Remove DDA support in UI
* [x] Update Release Note
* [x] Update LipidXplorer WikiThe DDA CSV support in LipidXplorer seems to be obsolete. It should be removed.
* [x] Remove DDA support in UI
* [x] Update Release Note
* [x] Update LipidXplorer WikiLipidXplorer 1.2.8https://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/3Remove Group samples from Import Source2019-09-11T09:50:53ZNils HoffmannRemove Group samples from Import SourceAlso ms input, and PIS spectrum.
* [x] Update Release Note
* [x] Update LipidXplorer WikiAlso ms input, and PIS spectrum.
* [x] Update Release Note
* [x] Update LipidXplorer WikiLipidXplorer 1.2.8https://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/15LX 1.2.8.2 - Interface - GUI not consistent fonts2019-09-11T09:49:25ZDominik SchwudkeLX 1.2.8.2 - Interface - GUI not consistent fontsIn the Tabs for the modules some visualization conspicuities are visible:
1) Import Settings
- Pixels below "selection"; different font style
- "MS1 offset", "PMO" line has different font style and font size
- scroll over "MS1 offset" ...In the Tabs for the modules some visualization conspicuities are visible:
1) Import Settings
- Pixels below "selection"; different font style
- "MS1 offset", "PMO" line has different font style and font size
- scroll over "MS1 offset" and "PMO" shows different style
2) Run
- Font style and font size is increased and not all strings are completly readable anymore
3) MS Tools
- same as above, font style and font size seems not to fitLipidXplorer 1.2.8https://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/8Check differences between RAW, mzXML and mzML data2019-09-11T05:59:08ZNils HoffmannCheck differences between RAW, mzXML and mzML dataI have compared mzXML and mzML scans (just one, exemplarily) for files 190321_Serum_Lipidextract_368723_01.mzML and 190321_Serum_Lipidextract_368723_01.mzXML. Comparison for scan numer 1 shows, that there are small deviations in the rep...I have compared mzXML and mzML scans (just one, exemplarily) for files 190321_Serum_Lipidextract_368723_01.mzML and 190321_Serum_Lipidextract_368723_01.mzXML. Comparison for scan numer 1 shows, that there are small deviations in the reported masses (fourth decimal position) and larger ones for the reported intensities (on average -2.3261 difference from mzML peaks to mzXML peaks). mzXML intensities seem to be higher all around, which also manifests itself in the comparative results with and without MSfilter and MSMSfilter.
[scan1_comparison_mzML_MzXML.xlsx](/uploads/d3e509ee91ad594fe56a055b3a0a2bb8/scan1_comparison_mzML_MzXML.xlsx)
[mzML_vs_mzXML_with_and_without_MSfilter_MSMSfilter.xlsx](/uploads/cea29b27acfc68cddb61cead2f795c6c/mzML_vs_mzXML_with_and_without_MSfilter_MSMSfilter.xlsx)
## Workflow Outline
### LipidXplorer 1.2.8
| MSFilter/MSMSfilter | Metric | Value | Input Format |
| ------ | ------ | ------ | ------ |
| 0 | No. of Peaks MS1 | | mzXML from PeakStrainer |
| | No. of Peaks MS2 | | |
| 0.6 | No. of Peaks MS1 || mzXML from PeakStrainer |
| | No. of Peaks MS2 | | |
| 0 | No. of Peaks MS1 |2123 | mzXML from msConvert |
| | No. of Peaks MS2 | 278162 | |
| 0.6 | No. of Peaks MS1 | 1887| mzXML from msConvert |
| | No. of Peaks MS2 |249344 | |
| 0 | No. of Peaks MS1 | 2126| mzML from msConvert |
| | No. of Peaks MS2 | 275956| |
| 0.6 | No. of Peaks MS1 |1884| mzML from msConvert |
| | No. of Peaks MS2 |246412 | |
RAW -> mzML || mzXML -> LX 1.2.7 || LX 1.2.8
LipidXplorer 1.2.8https://gitlab.isas.de/lifs-public/lipidxplorer/-/issues/14Remove "Choose Alignment Method"2019-08-23T14:22:45ZDominik SchwudkeRemove "Choose Alignment Method"Please remove under "Options" the "Choose Alignment Method" Menu.
It is generally not required and not used.Please remove under "Options" the "Choose Alignment Method" Menu.
It is generally not required and not used.LipidXplorer 1.2.8