Invalid refined mass error values in PPMErrorCharter

[alchemistmatt]

The mass errors shown in issue #1 are incorrect (they are far too large). For example

# mono PPMErrorCharterPython.exe -I:/data/MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02.mzid -EValue:1E-10 -Python

PPMErrorCharter, version 1.2.7109.23736 (June 19, 2019)
    Statistic                   Original    Refined
    MeanMassErrorPPM:              2.207    163.022
    MedianMassErrorPPM:            2.062      0.516
    StDev(Mean):                   2.961    267.748
    StDev(Median):                 2.964    313.205
    PPM Window for 99%: 0 +/-     10.955    940.131
    PPM Window for 99%: high:     10.955    940.131
    PPM Window for 99%:  low:     -6.832   -939.100

[alchemistmatt]

This is fixed via commit https://github.com/PNNL-Comp-Mass-Spec/PPMErrorCharter/commit/9d32729499e79ba0a6883f99291af5b911a667cb

New results for MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02:

PPMErrorCharter.exe -I:MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02.mzid.gz -EValue:1E-10 -Python

PPMErrorCharter, version 1.2.7111.20545 (June 21, 2019)

        Statistic                   Original    Refined
        MeanMassErrorPPM:              1.704     -0.103
        MedianMassErrorPPM:            2.355      0.009
        StDev(Mean):                   5.759      8.354
        StDev(Median):                 5.795      8.355
        PPM Window for 99%: 0 +/-     19.740     25.073
        PPM Window for 99%: high:     19.740     25.073
        PPM Window for 99%:  low:    -15.031    -25.054

Release 1.2.7111 includes an updated executable. https://github.com/PNNL-Comp-Mass-Spec/PPMErrorCharter/releases

Note: The mass errors shown above differ from those in Issue #1 most likely due to the use of a different FASTA file to search this data. David, please re-process your data using the updated PPMErrorCharterPython.exe and paste the results as a new comment on this issue.

[biodavidjm]

Same results:

mono PPMErrorCharterPython.exe -I:/data/MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02.mzid -EValue:1E-10
PPMErrorCharter, version 1.2.7111.20545 (June 21, 2019)

Using options:
 PSM results file: /data/MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02.mzid
 Spec EValue threshold: 1.0E-10
 PPM Error histogram bin size: 0.5
 Generating plots with OxyPlot

Creating plots for "MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02.mzid"
  Using fixed data file "/data/MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02_FIXED.mzML"

Loading data from the .mzid file
  6,290 PSMs passed the filters

Loading data from MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02_FIXED.mzML
  25% complete
  54% complete
  82% complete

    Statistic                   Original    Refined
    MeanMassErrorPPM:              2.207      0.143
    MedianMassErrorPPM:            2.035     -0.001
    StDev(Mean):                   2.961      2.941
    StDev(Median):                 2.966      2.944
    PPM Window for 99%: 0 +/-     10.932      8.834
    PPM Window for 99%: high:     10.932      8.833
    PPM Window for 99%:  low:     -6.863     -8.834

Using data points with original and refined MassError between -0.2 and 0.2 Da
Using data points with original and refined PpmError between -50 and 50 ppm

Removed 0 out-of-range items from the original 6,290 items.

  Assuming Python 3 is at /usr/bin/python3

  /usr/bin/python3 /app/PPMErrorCharter_Plotter.py /data/MZRefinery_Plotting_Metadata.txt
Reading metadata file: /data/MZRefinery_Plotting_Metadata.txt

Reading MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02_Histograms_TmpExportData.txt
Reading MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02_MassErrorsVsTime_TmpExportData.txt
Reading MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02_MassErrorsVsMass_TmpExportData.txt

Output: MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02_MZRefinery_Histograms.png

Plot "Mass error (PPM)" vs. "Original: Counts"
  87 data points

Mass error histogram created

Output: MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02_MZRefinery_MassErrors.png

Plot "Scan Time (minutes)" vs. "Original: Mass Error (PPM)" and
Plot "m/z" vs. "Original: Mass Error (PPM)"
  6,290 data points
  6,290 data points

Mass error trend plot created
Generated plots; see:
  /data/MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02/MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02_Histograms.png
and
  /data/MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02/MoTrPAC_Pilot_TMT_W_S1_01_12Oct17_Elm_AQ-17-09-02_MassErrors.png
Processing completed successfully