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compomics / denovogui

Graphical user interface for de novo sequencing of tandem mass spectra
http://compomics.github.io/projects/denovogui.html
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PepNovo PTM +42 not recognised #37

Closed animesh closed 7 years ago

animesh commented 7 years ago

Facing an error while running denovogui for the pepnovo+ err

hbarsnes commented 7 years ago

Hi Animesh,

Can you send me the DeNovoGUI log file? You'll finds it via the "Bug Report" option on the Help menu.

Best regards, Harald

animesh commented 7 years ago

Dear Harald,

Please find the attached bug-report. I can also share the files if the need be. But I suspect this is due to N-term Ac as dynamic PTM?

Regards,

Ani

--------------------------"The Answer Lies In The Genome"--------------------------

[[[ To any NSA and FBI agents reading my email: please consider ]]] [[[ whether defending the US Constitution against all enemies, ]]] [[[ foreign or domestic, requires you to follow Snowden's example. ]]] -rms

On Mon, Sep 4, 2017 at 2:36 PM, Harald Barsnes notifications@github.com wrote:

Hi Animesh,

Can you send me the DeNovoGUI log file? You'll finds it via the "Bug Report" option on the Help menu.

Best regards, Harald

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/denovogui/issues/37#issuecomment-326952558, or mute the thread https://github.com/notifications/unsubscribe-auth/AABT0WCbPEbECN47ChTvCSL5LDebE7CBks5se-7RgaJpZM4PKJvq .

Fri Sep 01 13:29:53 CEST 2017: DeNovoGUI version 1.15.11.

Fri Sep 01 14:06:13 CEST 2017: DeNovoGUI version 1.15.11.

Novor command: "C:\Program Files\Java\jdk1.8.0_121\jre\bin\java" -Xms128M -Xmx4096M -jar "F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor.jar" -p F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor_params.txt -m F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor_mods.txt -o "F:\promec\USERS\AnneVogel\DNovo\20170817_Anne_GelBand1.novor.csv" -f "F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1.mgf"

DirecTag command: F:\promec\DeNovoGUI-1.15.11\resources\DirecTag\windows_64bits\directag.exe F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1.mgf -cpus 16 -StaticMods "C 57.021464" -DynamicMods "N 0 0.984016 Q 1 0.984016 M 2 15.994915" -FragmentMzTolerance 0.002 -PrecursorMzTolerance 0.01 -TagLength 4 -MaxTagCount 10 -MaxPeakCount 100 -NumIntensityClasses 3 -TicCutoffPercentage 1.0 -AdjustPrecursorMass false -MinPrecursorAdjustment -0.5 -MaxPrecursorAdjustment 1.5 -PrecursorAdjustmentStep 0.1 -NumChargeStates 3 -UseChargeStateFromMS true -DuplicateSpectra true -DeisotopingMode 0 -IsotopeMzTolerance 0.25 -IsotopeMzTolerance 0.1 -MaxDynamicMods 2 -IntensityScoreWeight 1.0 -MzFidelityScoreWeight 1.0 -ComplementScoreWeight 1.0 -workdir F:\promec\USERS\AnneVogel\DNovo

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_1.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_2.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_3.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_4.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_5.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_6.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_7.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_8.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_9.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_10.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_11.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_12.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_13.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_14.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_15.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_16.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

pNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\pNovo\windows\pNovoplus.exe F:\promec\DeNovoGUI-1.15.11\resources\pNovo\windows\pnovo_params.txt ""

Novor command: "C:\Program Files\Java\jdk1.8.0_121\jre\bin\java" -Xms128M -Xmx4096M -jar "F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor.jar" -p F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor_params.txt -m F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor_mods.txt -o "F:\promec\USERS\AnneVogel\DNovo\20170817_Anne_GelBand2.novor.csv" -f "F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2.mgf"

DirecTag command: F:\promec\DeNovoGUI-1.15.11\resources\DirecTag\windows_64bits\directag.exe F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2.mgf -cpus 16 -StaticMods "C 57.021464" -DynamicMods "N 0 0.984016 Q 1 0.984016 M 2 15.994915" -FragmentMzTolerance 0.002 -PrecursorMzTolerance 0.01 -TagLength 4 -MaxTagCount 10 -MaxPeakCount 100 -NumIntensityClasses 3 -TicCutoffPercentage 1.0 -AdjustPrecursorMass false -MinPrecursorAdjustment -0.5 -MaxPrecursorAdjustment 1.5 -PrecursorAdjustmentStep 0.1 -NumChargeStates 3 -UseChargeStateFromMS true -DuplicateSpectra true -DeisotopingMode 0 -IsotopeMzTolerance 0.25 -IsotopeMzTolerance 0.1 -MaxDynamicMods 2 -IntensityScoreWeight 1.0 -MzFidelityScoreWeight 1.0 -ComplementScoreWeight 1.0 -workdir F:\promec\USERS\AnneVogel\DNovo

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_1.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_2.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_3.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_4.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_5.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_6.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_7.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_8.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_9.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_10.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_11.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_12.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_13.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_14.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_15.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_16.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

pNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\pNovo\windows\pNovoplus.exe F:\promec\DeNovoGUI-1.15.11\resources\pNovo\windows\pnovo_params.txt ""

Novor command: "C:\Program Files\Java\jdk1.8.0_121\jre\bin\java" -Xms128M -Xmx4096M -jar "F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor.jar" -p F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor_params.txt -m F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor_mods.txt -o "F:\promec\USERS\AnneVogel\DNovo\20170817_Anne_GelBand3.novor.csv" -f "F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3.mgf"

DirecTag command: F:\promec\DeNovoGUI-1.15.11\resources\DirecTag\windows_64bits\directag.exe F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3.mgf -cpus 16 -StaticMods "C 57.021464" -DynamicMods "N 0 0.984016 Q 1 0.984016 M 2 15.994915" -FragmentMzTolerance 0.002 -PrecursorMzTolerance 0.01 -TagLength 4 -MaxTagCount 10 -MaxPeakCount 100 -NumIntensityClasses 3 -TicCutoffPercentage 1.0 -AdjustPrecursorMass false -MinPrecursorAdjustment -0.5 -MaxPrecursorAdjustment 1.5 -PrecursorAdjustmentStep 0.1 -NumChargeStates 3 -UseChargeStateFromMS true -DuplicateSpectra true -DeisotopingMode 0 -IsotopeMzTolerance 0.25 -IsotopeMzTolerance 0.1 -MaxDynamicMods 2 -IntensityScoreWeight 1.0 -MzFidelityScoreWeight 1.0 -ComplementScoreWeight 1.0 -workdir F:\promec\USERS\AnneVogel\DNovo

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_1.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_2.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_3.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_4.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_5.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_6.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_7.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_8.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_9.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_10.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_11.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_12.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_13.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_14.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_15.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_16.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

pNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\pNovo\windows\pNovoplus.exe F:\promec\DeNovoGUI-1.15.11\resources\pNovo\windows\pnovo_params.txt ""

Novor command: "C:\Program Files\Java\jdk1.8.0_121\jre\bin\java" -Xms128M -Xmx4096M -jar "F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor.jar" -p F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor_params.txt -m F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor_mods.txt -o "F:\promec\USERS\AnneVogel\DNovo\20170817_Anne_GelBand4.novor.csv" -f "F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4.mgf"

DirecTag command: F:\promec\DeNovoGUI-1.15.11\resources\DirecTag\windows_64bits\directag.exe F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4.mgf -cpus 16 -StaticMods "C 57.021464" -DynamicMods "N 0 0.984016 Q 1 0.984016 M 2 15.994915" -FragmentMzTolerance 0.002 -PrecursorMzTolerance 0.01 -TagLength 4 -MaxTagCount 10 -MaxPeakCount 100 -NumIntensityClasses 3 -TicCutoffPercentage 1.0 -AdjustPrecursorMass false -MinPrecursorAdjustment -0.5 -MaxPrecursorAdjustment 1.5 -PrecursorAdjustmentStep 0.1 -NumChargeStates 3 -UseChargeStateFromMS true -DuplicateSpectra true -DeisotopingMode 0 -IsotopeMzTolerance 0.25 -IsotopeMzTolerance 0.1 -MaxDynamicMods 2 -IntensityScoreWeight 1.0 -MzFidelityScoreWeight 1.0 -ComplementScoreWeight 1.0 -workdir F:\promec\USERS\AnneVogel\DNovo

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_1.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_2.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_3.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_4.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_5.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_6.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_7.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_8.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_9.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_10.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_11.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_12.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_13.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_14.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_15.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_16.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

pNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\pNovo\windows\pNovoplus.exe F:\promec\DeNovoGUI-1.15.11\resources\pNovo\windows\pnovo_params.txt ""

Novor command: "C:\Program Files\Java\jdk1.8.0_121\jre\bin\java" -Xms128M -Xmx4096M -jar "F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor.jar" -p F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor_params.txt -m F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor_mods.txt -o "F:\promec\USERS\AnneVogel\DNovo\20170817_Anne_GelBand5.novor.csv" -f "F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5.mgf"

DirecTag command: F:\promec\DeNovoGUI-1.15.11\resources\DirecTag\windows_64bits\directag.exe F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5.mgf -cpus 16 -StaticMods "C 57.021464" -DynamicMods "N 0 0.984016 Q 1 0.984016 M 2 15.994915" -FragmentMzTolerance 0.002 -PrecursorMzTolerance 0.01 -TagLength 4 -MaxTagCount 10 -MaxPeakCount 100 -NumIntensityClasses 3 -TicCutoffPercentage 1.0 -AdjustPrecursorMass false -MinPrecursorAdjustment -0.5 -MaxPrecursorAdjustment 1.5 -PrecursorAdjustmentStep 0.1 -NumChargeStates 3 -UseChargeStateFromMS true -DuplicateSpectra true -DeisotopingMode 0 -IsotopeMzTolerance 0.25 -IsotopeMzTolerance 0.1 -MaxDynamicMods 2 -IntensityScoreWeight 1.0 -MzFidelityScoreWeight 1.0 -ComplementScoreWeight 1.0 -workdir F:\promec\USERS\AnneVogel\DNovo

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5_1.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5_2.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5_3.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5_4.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5_5.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5_6.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5_7.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5_8.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5_9.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5_10.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5_11.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5_12.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5_13.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5_14.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5_15.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand5_16.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

pNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\pNovo\windows\pNovoplus.exe F:\promec\DeNovoGUI-1.15.11\resources\pNovo\windows\pnovo_params.txt ""

Novor command: "C:\Program Files\Java\jdk1.8.0_121\jre\bin\java" -Xms128M -Xmx4096M -jar "F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor.jar" -p F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor_params.txt -m F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor_mods.txt -o "F:\promec\USERS\AnneVogel\DNovo\20170817_Anne_GelBand6.novor.csv" -f "F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6.mgf"

DirecTag command: F:\promec\DeNovoGUI-1.15.11\resources\DirecTag\windows_64bits\directag.exe F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6.mgf -cpus 16 -StaticMods "C 57.021464" -DynamicMods "N 0 0.984016 Q 1 0.984016 M 2 15.994915" -FragmentMzTolerance 0.002 -PrecursorMzTolerance 0.01 -TagLength 4 -MaxTagCount 10 -MaxPeakCount 100 -NumIntensityClasses 3 -TicCutoffPercentage 1.0 -AdjustPrecursorMass false -MinPrecursorAdjustment -0.5 -MaxPrecursorAdjustment 1.5 -PrecursorAdjustmentStep 0.1 -NumChargeStates 3 -UseChargeStateFromMS true -DuplicateSpectra true -DeisotopingMode 0 -IsotopeMzTolerance 0.25 -IsotopeMzTolerance 0.1 -MaxDynamicMods 2 -IntensityScoreWeight 1.0 -MzFidelityScoreWeight 1.0 -ComplementScoreWeight 1.0 -workdir F:\promec\USERS\AnneVogel\DNovo

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6_1.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6_2.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6_3.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6_4.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6_5.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6_6.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6_7.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6_8.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6_9.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6_10.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6_11.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6_12.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6_13.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6_14.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6_15.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand6_16.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

pNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\pNovo\windows\pNovoplus.exe F:\promec\DeNovoGUI-1.15.11\resources\pNovo\windows\pnovo_params.txt ""

Novor command: "C:\Program Files\Java\jdk1.8.0_121\jre\bin\java" -Xms128M -Xmx4096M -jar "F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor.jar" -p F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor_params.txt -m F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor_mods.txt -o "F:\promec\USERS\AnneVogel\DNovo\20170817_Anne_GelBand7.novor.csv" -f "F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7.mgf"

DirecTag command: F:\promec\DeNovoGUI-1.15.11\resources\DirecTag\windows_64bits\directag.exe F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7.mgf -cpus 16 -StaticMods "C 57.021464" -DynamicMods "N 0 0.984016 Q 1 0.984016 M 2 15.994915" -FragmentMzTolerance 0.002 -PrecursorMzTolerance 0.01 -TagLength 4 -MaxTagCount 10 -MaxPeakCount 100 -NumIntensityClasses 3 -TicCutoffPercentage 1.0 -AdjustPrecursorMass false -MinPrecursorAdjustment -0.5 -MaxPrecursorAdjustment 1.5 -PrecursorAdjustmentStep 0.1 -NumChargeStates 3 -UseChargeStateFromMS true -DuplicateSpectra true -DeisotopingMode 0 -IsotopeMzTolerance 0.25 -IsotopeMzTolerance 0.1 -MaxDynamicMods 2 -IntensityScoreWeight 1.0 -MzFidelityScoreWeight 1.0 -ComplementScoreWeight 1.0 -workdir F:\promec\USERS\AnneVogel\DNovo

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7_1.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7_2.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7_3.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7_4.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7_5.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7_6.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7_7.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7_8.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7_9.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7_10.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7_11.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7_12.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7_13.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7_14.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7_15.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand7_16.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

pNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\pNovo\windows\pNovoplus.exe F:\promec\DeNovoGUI-1.15.11\resources\pNovo\windows\pnovo_params.txt ""

Novor command: "C:\Program Files\Java\jdk1.8.0_121\jre\bin\java" -Xms128M -Xmx4096M -jar "F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor.jar" -p F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor_params.txt -m F:\promec\DeNovoGUI-1.15.11\resources\Novor\novor_mods.txt -o "F:\promec\USERS\AnneVogel\DNovo\20170817_Anne_GelBand8.novor.csv" -f "F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8.mgf"

DirecTag command: F:\promec\DeNovoGUI-1.15.11\resources\DirecTag\windows_64bits\directag.exe F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8.mgf -cpus 16 -StaticMods "C 57.021464" -DynamicMods "N 0 0.984016 Q 1 0.984016 M 2 15.994915" -FragmentMzTolerance 0.002 -PrecursorMzTolerance 0.01 -TagLength 4 -MaxTagCount 10 -MaxPeakCount 100 -NumIntensityClasses 3 -TicCutoffPercentage 1.0 -AdjustPrecursorMass false -MinPrecursorAdjustment -0.5 -MaxPrecursorAdjustment 1.5 -PrecursorAdjustmentStep 0.1 -NumChargeStates 3 -UseChargeStateFromMS true -DuplicateSpectra true -DeisotopingMode 0 -IsotopeMzTolerance 0.25 -IsotopeMzTolerance 0.1 -MaxDynamicMods 2 -IntensityScoreWeight 1.0 -MzFidelityScoreWeight 1.0 -ComplementScoreWeight 1.0 -workdir F:\promec\USERS\AnneVogel\DNovo

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8_1.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8_2.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8_3.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8_4.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8_5.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8_6.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8_7.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8_8.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8_9.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8_10.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8_11.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8_12.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8_13.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8_14.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8_15.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand8_16.mgf -model CID_IT_TRYP -PTMs C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

pNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\pNovo\windows\pNovoplus.exe F:\promec\DeNovoGUI-1.15.11\resources\pNovo\windows\pnovo_params.txt ""

Reindexing: Synechococcus7002CyanobaseCrap.fasta. java.lang.IllegalArgumentException: Accession numbers cannot contain quotation marks: 'SYNPCC7002_A0155 Deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase) (dUTP pyrophosphatase)'! Please check your FASTA file. at com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.createFastaIndex(SequenceFactory.java:796) at com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.getFastaIndex(SequenceFactory.java:708) at com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.getFastaIndex(SequenceFactory.java:638) at com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.loadFastaFile(SequenceFactory.java:579) at com.compomics.util.protein_sequences_manager.gui.SequenceDbDetailsDialog$3.run(SequenceDbDetailsDialog.java:355) Reindexing: Synechococcus7002CyanobaseCrap.fasta. Reindexing: Synechococcus7002CyanobaseCrap_concatenated_target_decoy.fasta. Reindexing: Synechococcus7002CyanobaseCrap.fasta. (changes in the file detected) Reindexing: Synechococcus7002CyanobaseCrap.fasta. java.lang.IllegalArgumentException: Non unique accession number found 'Tax'! Please check your FASTA file. at com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.createFastaIndex(SequenceFactory.java:801) at com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.getFastaIndex(SequenceFactory.java:708) at com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.getFastaIndex(SequenceFactory.java:638) at com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.loadFastaFile(SequenceFactory.java:579) at com.compomics.util.protein_sequences_manager.gui.SequenceDbDetailsDialog$3.run(SequenceDbDetailsDialog.java:355) Reindexing: Synechococcus7002CyanobaseCrap.fasta. (changes in the file detected) Reindexing: Synechococcus7002CyanobaseCrap.fasta. java.lang.IllegalArgumentException: Non unique accession number found 'Tax'! Please check your FASTA file. at com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.createFastaIndex(SequenceFactory.java:801) at com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.getFastaIndex(SequenceFactory.java:708) at com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.getFastaIndex(SequenceFactory.java:638) at com.compomics.util.experiment.identification.protein_sequences.SequenceFactory.loadFastaFile(SequenceFactory.java:579) at com.compomics.util.protein_sequences_manager.gui.SequenceDbDetailsDialog$3.run(SequenceDbDetailsDialog.java:355) Reindexing: Synechococcus7002CyanobaseCrap.fasta. (changes in the file detected) Reindexing: Synechococcus7002CyanobaseCrap.fasta. Reindexing: Synechococcus7002CyanobaseCrap_concatenated_target_decoy.fasta. (changes in the file detected) Reindexing: Synechococcus7002CyanobaseCrap_concatenated_target_decoy.fasta.

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_1.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_2.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_3.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_4.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_5.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_6.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_7.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_8.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_9.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_10.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_11.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_12.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_13.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_14.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_15.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand1_16.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_1.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_2.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_3.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_4.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_5.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_6.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_7.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_8.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_9.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_10.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_11.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_12.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_13.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_14.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_15.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand2_16.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_1.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_2.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_3.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_4.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_5.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_6.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_7.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_8.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_9.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_10.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_11.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_12.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_13.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_14.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_15.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand3_16.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_1.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_2.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_3.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_4.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_5.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_6.mgf -model CID_IT_TRYP -PTMs ^+42:C+57:N+1:Q+1:M+16 -fragment_tolerance 0.002 -num_solutions 10 -pm_tolerance 0.01 -use_spectrum_mz

PepNovo+ command: F:\promec\DeNovoGUI-1.15.11\resources\PepNovo\PepNovo_Windows.exe -file F:\promec\USERS\AnneVogel\20170817_Anne_GelBand4_7.mgf -

hbarsnes commented 7 years ago

Hi Ani,

Nothing interesting in the log file I'm afraid.

I can also share the files if the need be.

That would perhaps be the easiest.

But I suspect this is due to N-term Ac as dynamic PTM?

Most likely. But I'd need to look at the data to confirm.

Best regards, Harald

PS: When sharing files on the issue tracker it is much better if you upload them as files instead of copying the text, as this makes the issues much easier to read with a lot less scrolling required. ;)

animesh commented 7 years ago

Seems like attaching file to email is autoread in github, sorry about that Harald.

I have send you the files via gdrive, let me know if you don't get it. To reproduce this, you would need to add N-term Ac as Dynamic mod :)

Regards,

Ani

--------------------------"The Answer Lies In The Genome"--------------------------

[[[ To any NSA and FBI agents reading my email: please consider ]]] [[[ whether defending the US Constitution against all enemies, ]]] [[[ foreign or domestic, requires you to follow Snowden's example. ]]] -rms

On Mon, Sep 4, 2017 at 4:30 PM, Harald Barsnes notifications@github.com wrote:

Hi Ani,

Nothing interesting in the log file I'm afraid.

I can also share the files if the need be.

That would perhaps be the easiest.

But I suspect this is due to N-term Ac as dynamic PTM?

Most likely. But I'd need to look at the data to confirm.

Best regards, Harald

PS: When sharing files on the issue tracker it is much better if you upload them as files instead of copying the text, as this makes the issues much easier to read with a lot less scrolling required. ;)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/denovogui/issues/37#issuecomment-326976673, or mute the thread https://github.com/notifications/unsubscribe-auth/AABT0Urn8wxp2cVEVeu807bVfOe9BFfjks5sfAmhgaJpZM4PKJvq .

hbarsnes commented 7 years ago

Hi Ani,

I did not receive any emails with the links. Perhaps you can try sending them to my gmail address instead?

Best regards, Harald

hbarsnes commented 7 years ago

Hi Ani,

I have no problems loading the PepNovo+ results from the first mgf file you sent me (20170817_Anne_GelBand1.mgf), even after adding n-term acetylation as a variable modification. Could you try reproducing the error on a single mgf file?

And perhaps you can also send me the rest of your search settings so that we have the exact same settings?

Best regards, Harald

animesh commented 7 years ago

Strange, could it be because i am using the same output directory? Attached dnovo.txt is the parameter i am using. Also, to note that PepNovo+novor ran together.

hbarsnes commented 7 years ago

Hi Ani,

I've located and fixed the issue. The problem was that the PepNovo PTM mappings were not altered if you changed the parameter file between two de novo runs. Well, unless you restarted DeNovoGUI. Hence only the PTMs used in the first selected parameter file were supported when opening the results of the second de novo run, resulting in the above issue if the second run contained PTMs not included in the first run.

I've just released DeNovoGUI v1.15.12 which should solve the problem. If this is not the case, please let me know and I'll reopen the issue.

Best regards, Harald

animesh commented 7 years ago

Dear Harald,

I can confirm that both bugs seem to have been resolved for this case, Perfect!

Thanks and best regards,

Ani

--------------------------"The Answer Lies In The Genome"--------------------------

[[[ To any NSA and FBI agents reading my email: please consider ]]] [[[ whether defending the US Constitution against all enemies, ]]] [[[ foreign or domestic, requires you to follow Snowden's example. ]]] -rms

On Wed, Sep 6, 2017 at 3:16 PM, Harald Barsnes notifications@github.com wrote:

Hi Ani,

I've located and fixed the issue. The problem was that the PepNovo PTM mappings were not altered if you changed the parameter file between two de novo runs. Well, unless you restarted DeNovoGUI. Hence only the PTMs used in the first selected parameter file were supported when opening the results of the second de novo run, resulting in the above issue if the second run contained PTMs not included in the first run.

I've just released DeNovoGUI v1.15.12 which should solve the problem. If this is not the case, please let me know and I'll reopen the issue.

Best regards, Harald

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/compomics/denovogui/issues/37#issuecomment-327479631, or mute the thread https://github.com/notifications/unsubscribe-auth/AABT0ehu58UegqTzLEmvjrx-ol8kPIHGks5sfpsagaJpZM4PKJvq .