Viewing TIMS ToF data from Fragpipe

[yishai99]

Hi, I processed .d raw files with Fragpipe and wish to review the identifications.
It is not clear which raw files I should use because the data was read directly in Fragpipe and was not transformed to mzML.
Thanks,

Yishai

[KaiLiCn]

Hi Yishai,

Fragpipe now supports export results into PDV directly. You could click the "Open FragPipe-PDV viewer" on the "Run" panel after finishing the analysis in Fragpipe.

Kai

[yishai99]

Yes but I want to view data that has already been processed and FP is closed.On 19 Apr 2023, at 18:45, KaiLiCn ***@***.***> wrote: Hi Yishai, Fragpipe now supports export results into PDV directly. You could click the "Open FragPipe-PDV viewer" on the "Run" panel after finishing the analysis in Fragpipe. Kai —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>

[KaiLiCn]

If you want to visualize the closed result, you could point your result folder in the "Output dir" field on the "Run" panel and click the "Viewer" button:

Please make sure there are no files deleted in your result folder.

Kai

[yishai99]

I tried it now. I get an error saying: “There is no valid manifest file in your result folder”. As far as I can tell, no files have been moved. Thanks, Y

…

On 19 Apr 2023, at 19:01, KaiLiCn ***@***.***> wrote: If you want to visualize the closed result, you could point your result folder in the "Output dir" field on the "Run" panel and click the "Viewer" button: <https://user-images.githubusercontent.com/29800230/233133135-eef83d01-2a35-4913-af5f-0583247c4981.png> Please make sure there are no files deleted in your result folder. Kai — Reply to this email directly, view it on GitHub <#47 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE5PDY3FEN3STRFBCMVPGODXCAD5RANCNFSM6AAAAAAXDW4VQA>. You are receiving this because you authored the thread.

[KaiLiCn]

May I ask which version of Fragpipe you are using right now? 18.x or 19.x? Fragpipe 19 changed some file names in the result folder. If you open the old version result with the new version of Fragpipe, it might cause some problems.

If it's ok, could you share your log_*.txt files and *-manifest files in the result folder with me?

[yishai99]

I am working with 19.1 I tried visualizing the results with v 18 and got a different error: “Failed to parse results, please check your file” Attached are the files you asked. Y  

On 20 Apr 2023, at 17:54, KaiLiCn ***@***.***> wrote: May I ask which version of Fragpipe you are using right now? 18.x or 19.x? Fragpipe 19 changed some file names in the result folder. If you open the old version result with the new version of Fragpipe, it might cause some problems. If it's ok, could you share your log_*.txt files and *-manifest files in the result folder with me? — Reply to this email directly, view it on GitHub <#47 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE5PDYYZ7LGKHDIWAF45NXTXCFEZJANCNFSM6AAAAAAXDW4VQA>. You are receiving this because you authored the thread.

System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK Version info: FragPipe version 18.0 MSFragger version 3.5 Philosopher version 4.4.0 LCMS files: Experiment/Group: TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11 - D:\16689\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11.d DDA Experiment/Group: TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11 - D:\16689\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11.d DDA Experiment/Group: TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15 - D:\16689\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15.d DDA Experiment/Group: TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11 - D:\16689\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11.d DDA Experiment/Group: TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11 - D:\16689\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11.d DDA Experiment/Group: TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10 - D:\16689\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10.d DDA Experiment/Group: TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11 - D:\16689\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11.d DDA Experiment/Group: TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13 - D:\16689\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13.d DDA Experiment/Group: TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13 - D:\16689\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13.d DDA Experiment/Group: TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11 - D:\16689\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11.d DDA 129 commands to execute: CheckCentroid C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -Xmx110G -cp "C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\batmass-io-1.25.5.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\16689\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11.d 30 WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\df9afa72-7d48-4465-919f-e9785880e289 WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\e8b5a0f7-bc86-47bf-81af-ec1c825bed3b WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\fef39ff5-b4e9-48e4-a21e-615f08194d95 WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\680250dd-6239-4d17-b106-148f44e0315b WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\6748c66f-2fbc-434a-ba5b-bfec1c8aac53 WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\941a606f-189c-42e0-90a7-5ae1c50f8bd5 WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\3e08a3c9-6c5e-4af3-84e1-71cd6b04cf89 WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\d393af7b-b5f1-4e24-8c86-31a5e33e929c WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\daf2752f-cbbc-4bc6-9bc6-23c40ba629f1 WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\a0014c98-fe80-45b7-88b1-52d613c3a8ff WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\protolab\AppData\Local\Temp\acda00b7-7c10-478e-8eda-00a668779710 MSFragger [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx110G C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.5\MSFragger-3.5.jar H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\fragger.params D:\16689\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11.d D:\16689\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11.d D:\16689\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15.d D:\16689\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11.d D:\16689\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11.d D:\16689\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10.d D:\16689\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11.d D:\16689\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13.d D:\16689\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13.d D:\16689\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11.d MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11.pepXML H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11.pin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11.pepXML H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11.pin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15.pepXML H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15.pin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11.pepXML H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11.pin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11.pepXML H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11.pin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10.pepXML H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10.pin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11.pepXML H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11.pin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13.pepXML H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13.pin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13.pepXML H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13.pin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11.pepXML H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\16689\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11.pin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11.pin MSBooster [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -Xmx110G -cp "C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\msbooster-1.1.4.jar;C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\smile-core-2.6.0.jar;C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\smile-math-2.6.0.jar;C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\batmass-io-1.25.5.jar" Features.MainClass --paramsList H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\msbooster_params.txt Percolator [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11_percolator_target_psms.tsv --decoy-results-psms TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11_percolator_decoy_psms.tsv TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11_edited.pin Percolator [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11_percolator_target_psms.tsv --decoy-results-psms TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11_percolator_decoy_psms.tsv TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11_edited.pin Percolator [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13_percolator_target_psms.tsv --decoy-results-psms TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13_percolator_decoy_psms.tsv TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13_edited.pin Percolator [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15_percolator_target_psms.tsv --decoy-results-psms TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15_percolator_decoy_psms.tsv TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15_edited.pin Percolator [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11_percolator_target_psms.tsv --decoy-results-psms TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11_percolator_decoy_psms.tsv TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11_edited.pin Percolator [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11_percolator_target_psms.tsv --decoy-results-psms TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11_percolator_decoy_psms.tsv TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11_edited.pin Percolator [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13_percolator_target_psms.tsv --decoy-results-psms TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13_percolator_decoy_psms.tsv TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13_edited.pin Percolator [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11_percolator_target_psms.tsv --decoy-results-psms TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11_percolator_decoy_psms.tsv TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11_edited.pin Percolator [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10_percolator_target_psms.tsv --decoy-results-psms TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10_percolator_decoy_psms.tsv TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10_edited.pin Percolator [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11_percolator_target_psms.tsv --decoy-results-psms TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11_percolator_decoy_psms.tsv TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11_edited.pin Percolator: Convert to pepxml [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11.pin TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11 TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11_percolator_target_psms.tsv TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11_percolator_decoy_psms.tsv interact-TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11.pin TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11 TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11_percolator_target_psms.tsv TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11_percolator_decoy_psms.tsv interact-TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13.pin TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13 TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13_percolator_target_psms.tsv TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13_percolator_decoy_psms.tsv interact-TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15.pin TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15 TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15_percolator_target_psms.tsv TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15_percolator_decoy_psms.tsv interact-TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11.pin TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11 TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11_percolator_target_psms.tsv TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11_percolator_decoy_psms.tsv interact-TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11.pin TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11 TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11_percolator_target_psms.tsv TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11_percolator_decoy_psms.tsv interact-TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13.pin TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13 TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13_percolator_target_psms.tsv TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13_percolator_decoy_psms.tsv interact-TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11.pin TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11 TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11_percolator_target_psms.tsv TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11_percolator_decoy_psms.tsv interact-TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10.pin TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10 TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10_percolator_target_psms.tsv TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10_percolator_decoy_psms.tsv interact-TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11.pin TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11 TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11_percolator_target_psms.tsv TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11_percolator_decoy_psms.tsv interact-TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar com.github.chhh.utils.FileDelete H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11_percolator_decoy_psms.tsv ProteinProphet [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe database --annotate H:\Proteomics\Databases\2022_Working_general_DBs\Bovine\2022-09-12-decoys-contam-Bos_Taurus_UP22.fasta.fas --prefix rev_ PhilosopherDbAnnotate [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe database --annotate H:\Proteomics\Databases\2022_Working_general_DBs\Bovine\2022-09-12-decoys-contam-Bos_Taurus_UP22.fasta.fas --prefix rev_ PhilosopherDbAnnotate [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe database --annotate H:\Proteomics\Databases\2022_Working_general_DBs\Bovine\2022-09-12-decoys-contam-Bos_Taurus_UP22.fasta.fas --prefix rev_ PhilosopherDbAnnotate [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe database --annotate H:\Proteomics\Databases\2022_Working_general_DBs\Bovine\2022-09-12-decoys-contam-Bos_Taurus_UP22.fasta.fas --prefix rev_ PhilosopherDbAnnotate [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe database --annotate H:\Proteomics\Databases\2022_Working_general_DBs\Bovine\2022-09-12-decoys-contam-Bos_Taurus_UP22.fasta.fas --prefix rev_ PhilosopherDbAnnotate [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe database --annotate H:\Proteomics\Databases\2022_Working_general_DBs\Bovine\2022-09-12-decoys-contam-Bos_Taurus_UP22.fasta.fas --prefix rev_ PhilosopherDbAnnotate [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe database --annotate H:\Proteomics\Databases\2022_Working_general_DBs\Bovine\2022-09-12-decoys-contam-Bos_Taurus_UP22.fasta.fas --prefix rev_ PhilosopherDbAnnotate [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe database --annotate H:\Proteomics\Databases\2022_Working_general_DBs\Bovine\2022-09-12-decoys-contam-Bos_Taurus_UP22.fasta.fas --prefix rev_ PhilosopherDbAnnotate [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe database --annotate H:\Proteomics\Databases\2022_Working_general_DBs\Bovine\2022-09-12-decoys-contam-Bos_Taurus_UP22.fasta.fas --prefix rev_ PhilosopherDbAnnotate [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe database --annotate H:\Proteomics\Databases\2022_Working_general_DBs\Bovine\2022-09-12-decoys-contam-Bos_Taurus_UP22.fasta.fas --prefix rev_ PhilosopherDbAnnotate [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe database --annotate H:\Proteomics\Databases\2022_Working_general_DBs\Bovine\2022-09-12-decoys-contam-Bos_Taurus_UP22.fasta.fas --prefix rev_ PhilosopherFilter [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11 --protxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\combined.prot.xml --razor PhilosopherFilter [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11 --protxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\combined.prot.xml --razorbin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11\.meta\razor.bin PhilosopherFilter [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15 --protxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\combined.prot.xml --razorbin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11\.meta\razor.bin PhilosopherFilter [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11 --protxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\combined.prot.xml --razorbin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11\.meta\razor.bin PhilosopherFilter [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11 --protxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\combined.prot.xml --razorbin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11\.meta\razor.bin PhilosopherFilter [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10 --protxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\combined.prot.xml --razorbin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11\.meta\razor.bin PhilosopherFilter [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11 --protxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\combined.prot.xml --razorbin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11\.meta\razor.bin PhilosopherFilter [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13 --protxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\combined.prot.xml --razorbin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11\.meta\razor.bin PhilosopherFilter [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13 --protxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\combined.prot.xml --razorbin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11\.meta\razor.bin PhilosopherFilter [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe filter --sequential --prot 0.01 --tag rev_ --pepxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11 --protxml H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\combined.prot.xml --razorbin H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11\.meta\razor.bin PhilosopherReport [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe report WorkspaceClean [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck IonQuant [Work dir: H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -Xmx110G -Dlibs.bruker.dir="C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.5\ext\bruker" -Dlibs.thermo.dir="C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.5\ext\thermo" -cp "C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\jfreechart-1.5.3.jar;C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\batmass-io-1.25.5.jar;C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\IonQuant-1.8.0.jar" ionquant.IonQuant --threads 30 --ionmobility 1 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 100000 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\filelist_ionquant.txt ~~~~~~~~~~~~~~~~~~~~~~ Execution order: Cmd: [START], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] Cmd: [CheckCentroid], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] Cmd: [WorkspaceCleanInit], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11] Cmd: [WorkspaceCleanInit], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11] Cmd: [WorkspaceCleanInit], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15] Cmd: [WorkspaceCleanInit], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11] Cmd: [WorkspaceCleanInit], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11] Cmd: [WorkspaceCleanInit], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13] Cmd: [WorkspaceCleanInit], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13] Cmd: [WorkspaceCleanInit], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11] Cmd: [WorkspaceCleanInit], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11] Cmd: [WorkspaceCleanInit], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10] Cmd: [WorkspaceCleanInit], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] Cmd: [MSFragger], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] Cmd: [MSBooster], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] Cmd: [Percolator], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] Cmd: [ProteinProphet], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] Cmd: [PhilosopherDbAnnotate], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] Cmd: [PhilosopherFilter], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] Cmd: [PhilosopherReport], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] Cmd: [WorkspaceClean], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_2-cow1_BCP_11-Sep-22_05-17-11] Cmd: [WorkspaceClean], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_4-cow2_BCP_11-Sep-22_03-50-11] Cmd: [WorkspaceClean], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_11-cow5_CTL_10-Sep-22_23-30-15] Cmd: [WorkspaceClean], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_12-cow5_BCP_11-Sep-22_08-11-11] Cmd: [WorkspaceClean], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_10-cow4_BCP_11-Sep-22_00-56-11] Cmd: [WorkspaceClean], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_7-cow3_CTL_11-Sep-22_12-32-13] Cmd: [WorkspaceClean], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_8-cow3_BCP_11-Sep-22_06-44-13] Cmd: [WorkspaceClean], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_9-cow4_CTL_11-Sep-22_02-23-11] Cmd: [WorkspaceClean], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_1-cow1_CTL_11-Sep-22_09-38-11] Cmd: [WorkspaceClean], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results\TTP_MZA_16689_3-cow2_CTL_11-Sep-22_11-05-10] Cmd: [WorkspaceClean], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] Cmd: [IonQuant], Work dir: [H:\Proteomics\Projects\Zachut_Volcani\INCPM_16689\Results] ~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~Sample of H:\Proteomics\Databases\2022_Working_general_DBs\Bovine\2022-09-12-decoys-contam-Bos_Taurus_UP22.fasta.fas~~~~~~~

contam_sp|O77727|K1C15_SHEEP Keratin, type I cytoskeletal 15 OS=Ovis aries GN=KRT15 PE=2 SV=1 rev_sp|Q2KIU7|RSPH9_BOVIN Radial spoke head protein 9 homolog OS=Bos taurus OX=9913 GN=RSPH9 PE=2 SV=1 rev_tr|A0A3Q1LMH1|A0A3Q1LMH1_BOVIN PAT1 homolog 1, processing body mRNA decay factor OS=Bos taurus OX=9913 GN=PATL1 PE=3 SV=1 rev_tr|A0A3Q1M0X6|A0A3Q1M0X6_BOVIN Dmx like 1 OS=Bos taurus OX=9913 GN=DMXL1 PE=4 SV=1 rev_tr|A0A3Q1ME09|A0A3Q1ME09_BOVIN Microtubule actin crosslinking factor 1 OS=Bos taurus OX=9913 GN=MACF1 PE=1 SV=1 rev_tr|A0A3Q1MU04|A0A3Q1MU04_BOVIN Amyloid beta protein binding family B member 1 OS=Bos taurus OX=9913 GN=APBB1 PE=4 SV=1 rev_tr|A0JNG1|A0JNG1_BOVIN Cordon-bleu WH2 repeat protein OS=Bos taurus OX=9913 GN=COBL PE=2 SV=1 rev_tr|E1BHM7|E1BHM7_BOVIN Ring finger protein 216 OS=Bos taurus OX=9913 GN=RNF216 PE=4 SV=1 rev_tr|F1MN39|F1MN39_BOVIN Interferon related developmental regulator 1 OS=Bos taurus OX=9913 GN=IFRD1 PE=3 SV=1 rev_tr|F6QJG7|F6QJG7_BOVIN Zona pellucida binding protein 2 OS=Bos taurus OX=9913 GN=ZPBP2 PE=3 SV=1 rev_tr|Q7YRE6|Q7YRE6_BOVIN GDP-fucose protein O-fucosyltransferase 1 OS=Bos taurus OX=9913 GN=POFUT1 PE=2 SV=1 sp|Q2KJ56|HOME1_BOVIN Homer protein homolog 1 OS=Bos taurus OX=9913 GN=HOMER1 PE=2 SV=1 tr|A0A3Q1LMN4|A0A3Q1LMN4_BOVIN Eva-1 homolog C OS=Bos taurus OX=9913 GN=EVA1C PE=3 SV=1 tr|A0A3Q1M136|A0A3Q1M136_BOVIN HEAT repeat containing 5B OS=Bos taurus OX=9913 GN=HEATR5B PE=3 SV=1 tr|A0A3Q1ME68|A0A3Q1ME68_BOVIN Protein-tyrosine-phosphatase OS=Bos taurus OX=9913 GN=PTPRT PE=3 SV=1 tr|A0A3Q1MUA7|A0A3Q1MUA7_BOVIN G_PROTEIN_RECEP_F1_2 domain-containing protein OS=Bos taurus OX=9913 PE=4 SV=1 tr|A1L528|A1L528_BOVIN RAB1A, member RAS onco family OS=Bos taurus OX=9913 GN=RAB1A PE=1 SV=1 tr|E1BHU9|E1BHU9_BOVIN Adenylate cyclase type 5 OS=Bos taurus OX=9913 GN=ADCY5 PE=3 SV=3 tr|F1MNB9|F1MNB9_BOVIN LysM and putative peptidoglycan-binding domain-containing protein 1 OS=Bos taurus OX=9913 GN=LYSMD1 PE=4 SV=1 tr|F6QSN7|F6QSN7_BOVIN Zinc finger protein 226 OS=Bos taurus OX=9913 GN=ZNF226 PE=4 SV=1 tr|W8QEC7|W8QEC7_BOVIN Nuclear factor 1 OS=Bos taurus OX=9913 GN=NFIX PE=2 SV=1

~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ fragpipe.config ~~~~~~~~~ # FragPipe v18.0ui state cache # Please edit the following path to point to the correct location. # In Windows, please replace single '\' with '\\' database.db-path=H\:\\Proteomics\\Databases\\2022_Working_general_DBs\\Bovine\\2022-09-12-decoys-contam-Bos_Taurus_UP22.fasta.fas Table.editor=0 crystalc.run-crystalc=false database.decoy-tag=rev_ diann.fragpipe.cmd-opts= diann.library= diann.q-value=0.01 diann.quantification-strategy=3 diann.run-dia-nn=false diann.run-specific-protein-q-value=0.01 diann.unrelated-runs=false diann.use-predicted-spectra=false diaumpire.AdjustFragIntensity=true diaumpire.BoostComplementaryIon=false diaumpire.CorrThreshold=0 diaumpire.DeltaApex=0.2 diaumpire.ExportPrecursorPeak=false diaumpire.Q1=true diaumpire.Q2=true diaumpire.Q3=true diaumpire.RFmax=500 diaumpire.RPmax=25 diaumpire.RTOverlap=0.3 diaumpire.SE.EstimateBG=false diaumpire.SE.IsoPattern=0.3 diaumpire.SE.MS1PPM=10 diaumpire.SE.MS2PPM=20 diaumpire.SE.MS2SN=1.1 diaumpire.SE.MassDefectFilter=true diaumpire.SE.MassDefectOffset=0.1 diaumpire.SE.NoMissedScan=1 diaumpire.SE.SN=1.1 diaumpire.run-diaumpire=false fragpipe-config.bin-ionquant=C\:\\Users\\protolab\\Downloads\\FragPipe-jre-18.0\\fragpipe\\tools\\IonQuant-1.8.0.jar fragpipe-config.bin-msfragger=C\:\\Users\\protolab\\Downloads\\FragPipe-jre-18.0\\fragpipe\\tools\\MSFragger-3.5\\MSFragger-3.5.jar fragpipe-config.bin-philosopher=C\:\\Users\\protolab\\Downloads\\FragPipe-jre-18.0\\fragpipe\\tools\\philosopher_v4.4.0_windows_amd64\\philosopher.exe fragpipe-config.bin-python=C\:\\ProgramData\\Anaconda3\\python freequant.mz-tol=10 freequant.rt-tol=0.4 freequant.run-freequant=false ionquant.excludemods= ionquant.heavy= ionquant.imtol=0.05

[KaiLiCn]

FragPipe 19 changed a lot in result folder structure. Based on your log file, this is the result generated by FragPipe 18. If you want to visualize this result, please try to use FragPipe 18. If you met the error, please try to replace the PDV in v18 with this one https://github.com/Nesvilab/FragPipe-PDV/releases/tag/V1.0.3 following the tutorial https://github.com/Nesvilab/FragPipe-PDV/blob/master/README.md . We have stopped the support of v18, please use the latest FragPipe in the future analysis.

Kai