sjr24 commented 3 years ago

Greetings,

The following error occurs during SpecLibGen of the DIA-U track in FragPipe.

SpecLibGen [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU] C:\ProgramData\Anaconda3\python.exe -u C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py C:\Users\srice\Downloads\FragPipe-14.0\2021-02-24-decoys-reviewed-contam-UP000005640.fas C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3_calibrated.mgf;C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3_uncalibrated.mgf;C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_calibrated.mgf;C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_uncalibrated.mgf;C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_calibrated.mgf;C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_uncalibrated.mgf C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU True unused use_easypqp ciRT 7 "--rt_lowess_fraction 0.01" Using (un)calibrated.mgfs. Spectral library building Commands to execute: 'C:\ProgramData\Anaconda3\Scripts\easypqp.exe' convert --pepxml 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\interact.pep.xml' --spectra 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_uncalibrated.mgf' --exclude-range -1.5,3.5 --psms 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.psmpkl --peaks 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.peakpkl 'C:\ProgramData\Anaconda3\Scripts\easypqp.exe' convert --pepxml 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\interact.pep.xml' --spectra 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_uncalibrated.mgf' --exclude-range -1.5,3.5 --psms 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.psmpkl --peaks 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.peakpkl 'C:\ProgramData\Anaconda3\Scripts\easypqp.exe' convert --pepxml 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\interact.pep.xml' --spectra 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3_calibrated.mgf' --exclude-range -1.5,3.5 --psms 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.psmpkl --peaks 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.peakpkl 'C:\ProgramData\Anaconda3\Scripts\easypqp.exe' library --psmtsv 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\psm.tsv' --peptidetsv 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\peptide.tsv' --rt_reference 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\irt.tsv' --out easypqp_lib_openswath.tsv --rt_lowess_fraction 0.01 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.psmpkl' 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.psmpkl' 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.psmpkl' 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.peakpkl' 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.peakpkl' 'C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.peakpkl'


easypqp, version 0.1.10
Executing ['C:\\ProgramData\\Anaconda3\\Scripts\\easypqp.exe', 'convert', '--pepxml', 'C:\\Users\\srice\\Downloads\\HeLa_Evosep_diaPASEF_RAW\\diaU\\interact.pep.xml', '--spectra', 'C:\\Users\\srice\\Downloads\\HeLa_Evosep_diaPASEF_RAW\\diaU\\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_uncalibrated.mgf', '--exclude-range', '-1.5,3.5', '--psms', '20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.psmpkl', '--peaks', '20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.peakpkl']
Executing ['C:\\ProgramData\\Anaconda3\\Scripts\\easypqp.exe', 'convert', '--pepxml', 'C:\\Users\\srice\\Downloads\\HeLa_Evosep_diaPASEF_RAW\\diaU\\interact.pep.xml', '--spectra', 'C:\\Users\\srice\\Downloads\\HeLa_Evosep_diaPASEF_RAW\\diaU\\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_uncalibrated.mgf', '--exclude-range', '-1.5,3.5', '--psms', '20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.psmpkl', '--peaks', '20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.peakpkl']
Executing ['C:\\ProgramData\\Anaconda3\\Scripts\\easypqp.exe', 'convert', '--pepxml', 'C:\\Users\\srice\\Downloads\\HeLa_Evosep_diaPASEF_RAW\\diaU\\interact.pep.xml', '--spectra', 'C:\\Users\\srice\\Downloads\\HeLa_Evosep_diaPASEF_RAW\\diaU\\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3_calibrated.mgf', '--exclude-range', '-1.5,3.5', '--psms', '20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.psmpkl', '--peaks', '20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.peakpkl']
EasyPQP convert error BEGIN
Info: Converting C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\interact.pep.xml.
Info: Parsing run 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.
Info: Parsing pepXML.
Info: Generate theoretical spectra.
Info: Processing spectra from file C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_uncalibrated.mgf.
Traceback (most recent call last):
  File "c:\programdata\anaconda3\lib\runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "c:\programdata\anaconda3\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "C:\ProgramData\Anaconda3\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 782, in main
    rv = self.invoke(ctx)
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 1289, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "c:\programdata\anaconda3\lib\site-packages\easypqp\main.py", line 58, in convert
    psms, peaks = conversion(pepxmlfile, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses)
  File "c:\programdata\anaconda3\lib\site-packages\easypqp\convert.py", line 606, in conversion
    peaks = read_mgf(spectralfile, psms[['scan_id', 'modified_peptide', 'precursor_charge']], theoretical, max_delta_ppm)
  File "c:\programdata\anaconda3\lib\site-packages\easypqp\convert.py", line 474, in read_mgf
    mz_intensity_array = tims_data[scan_id]
KeyError: 12
EasyPQP convert error END
EasyPQP convert error BEGIN
Info: Converting C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\interact.pep.xml.
Info: Parsing run 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.
Info: Parsing pepXML.
Info: Generate theoretical spectra.
Info: Processing spectra from file C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_uncalibrated.mgf.
Traceback (most recent call last):
  File "c:\programdata\anaconda3\lib\runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "c:\programdata\anaconda3\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "C:\ProgramData\Anaconda3\Scripts\easypqp.exe\__main__.py", line 7, in <module>
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 782, in main
    rv = self.invoke(ctx)
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 1289, in invoke
    rv.append(sub_ctx.command.invoke(sub_ctx))
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "c:\programdata\anaconda3\lib\site-packages\click\core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "c:\programdata\anaconda3\lib\site-packages\easypqp\main.py", line 58, in convert
    psms, peaks = conversion(pepxmlfile, spectralfile, unimodfile, exclude_range, max_delta_unimod, max_delta_ppm, enable_unannotated, enable_massdiff, fragment_types, fragment_charges, enable_specific_losses, enable_unspecific_losses)
  File "c:\programdata\anaconda3\lib\site-packages\easypqp\convert.py", line 606, in conversion
    peaks = read_mgf(spectralfile, psms[['scan_id', 'modified_peptide', 'precursor_charge']], theoretical, max_delta_ppm)
  File "c:\programdata\anaconda3\lib\site-packages\easypqp\convert.py", line 474, in read_mgf
    mz_intensity_array = tims_data[scan_id]
KeyError: 1
Traceback (most recent call last):
  File "C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\..\tools\speclib\gen_con_spec_lib.py", line 849, in <module>
    main_easypqp()
  File "C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\..\tools\speclib\gen_con_spec_lib.py", line 675, in main_easypqp
    assert all(p.returncode == 0 for p in procs)
AssertionError
EasyPQP convert error END
Process 'SpecLibGen' finished, exit code: 1
Process returned non-zero exit code, stopping

fcyu commented 3 years ago

Can you send us the whole log?

Best,

Fengchao

sjr24 commented 3 years ago

Fengchao,

I attached the log file, diau log file, and an easypqp log file.

Thanks,

Shawn

From: Fengchao [mailto:notifications@github.com] Sent: Friday, February 26, 2021 12:40 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Rice, Shawn srice@pennstatehealth.psu.edu; Author author@noreply.github.com Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

Attention: This email originated outside of Penn State Health. Use caution when clicking links or opening attachments.

Can you send us the whole log?

Best,

Fengchao

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/Nesvilab/FragPipe/issues/311*issuecomment-786792132__;Iw!!Ls64Rlj6!nnoHD9CUW2P0dQs9qVUMlq3XWfKWDunFIcAlqbML05iTOfUNcaADMyFdEfzMbeT0yMcvHA$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AJMH2PXMQZW7UNJVIMOWCG3TA7MIZANCNFSM4YI2PKWQ__;!!Ls64Rlj6!nnoHD9CUW2P0dQs9qVUMlq3XWfKWDunFIcAlqbML05iTOfUNcaADMyFdEfzMbeTERnCEZQ$.

System OS: Windows 10, Architecture: AMD64 Java Info: 12.0.1, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation

Version info: FragPipe version 14.0 MSFragger version 3.1.1 Philosopher version 3.4.13 (build 1611589727)

LCMS files: Experiment/Group:

C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.mzXML

44 commands to execute: UmpireSe java -jar C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib..\tools\dia_umpire_se-2.1.5.jar C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.mzXML C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\umpire-se_2021-02-26_12-15-03.params UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\diaumpire_se.log C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\diaumpire_se.log UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Peak C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Peak UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.DIAWindowsFS C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.DIAWindowsFS UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.RTidxFS C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.RTidxFS UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanClusterMapping_Q1 C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanClusterMapping_Q1 UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanClusterMapping_Q2 C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanClusterMapping_Q2 UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanClusterMapping_Q3 C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanClusterMapping_Q3 UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanidxFS C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanidxFS UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanPosFS C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanPosFS UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanRTFS C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanRTFS UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_diasetting.ser C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_diasetting.ser UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_params.ser C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_params.ser UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.mgf C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.mgf UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.mgf C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.mgf UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.mgf C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.mgf UmpireSe [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU] C:\Program Files (x86)\ProteoWizard 3.0.18353 64-bit\msconvert.exe --verbose --32 --zlib --mzXML --outdir C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.mgf UmpireSe [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU] C:\Program Files (x86)\ProteoWizard 3.0.18353 64-bit\msconvert.exe --verbose --32 --zlib --mzXML --outdir C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.mgf UmpireSe [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU] C:\Program Files (x86)\ProteoWizard 3.0.18353 64-bit\msconvert.exe --verbose --32 --zlib --mzXML --outdir C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.mgf UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Peak UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.DIAWindowsFS UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.RTidxFS UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanClusterMapping_Q1 UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanClusterMapping_Q2 UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanClusterMapping_Q3 UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanidxFS UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanPosFS UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.ScanRTFS UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_diasetting.ser UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_params.ser UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.mgf UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.mgf UmpireSe java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.mgf WorkspaceCleanInit [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU] C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU] C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck MsFragger [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU] java -jar -Dfile.encoding=UTF-8 -Xmx21G C:\Users\srice\Downloads\FragPipe-14.0\bin\fragpipe\bin\MSFragger-3.1.1\MSFragger-3.1.1.jar C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\fragger.params C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.mzXML C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.mzXML C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.mzXML PeptideProphet [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEFRAW\diaU] C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\Users\srice\Downloads\FragPipe-14.0\2021-02-24-decoys-reviewed-contam-UP000005640.fas --combine 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.pepXML 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.pepXML 20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.pepXML Rewrite pepxml [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU] java -cp C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\interact.pep.xml C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3.mzXML C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2.mzXML C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1.mzXML ProteinProphet [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU] C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\interact.pep.xml PhilosopherDbAnnotate [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEFRAW\diaU] C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\Users\srice\Downloads\FragPipe-14.0\2021-02-24-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherFilter [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEFRAW\diaU] C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --prot 0.01 --tag rev --pepxml C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU --protxml C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\combined.prot.xml PhilosopherReport [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU] C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe report WorkspaceClean [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU] C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck SpecLibGen [Work dir: C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU] C:\ProgramData\Anaconda3\python.exe -u C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib..\tools\speclib\gen_con_spec_lib.py C:\Users\srice\Downloads\FragPipe-14.0\2021-02-24-decoys-reviewed-contam-UP000005640.fas C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3_calibrated.mgf;C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q3_uncalibrated.mgf;C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_calibrated.mgf;C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_uncalibrated.mgf;C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_calibrated.mgf;C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_uncalibrated.mgf C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU True unused use_easypqp ciRT 7 "--rt_lowess_fraction 0.01"


Execution order:

    Cmd: [START], Work dir: [C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU]
    Cmd: [UmpireSe], Work dir: [C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU]
    Cmd: [MsFragger], Work dir: [C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU]
    Cmd: [PeptideProphet], Work dir: [C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU]
    Cmd: [ProteinProphet], Work dir: [C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU]
    Cmd: [PhilosopherDbAnnotate], Work dir: [C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU]
    Cmd: [PhilosopherFilter], Work dir: [C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU]
    Cmd: [PhilosopherReport], Work dir: [C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU]
    Cmd: [WorkspaceClean], Work dir: [C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU]
    Cmd: [SpecLibGen], Work dir: [C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU]

# FragPipe v14.0ui state cache

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0
DeltaApex=0.3
RFmax=500
RPmax=25
RTOverlap=0.3
SE.EstimateBG=false
SE.MS1PPM=15
SE.MS2PPM=25
SE.MS2SN=1.1
SE.MaxCurveRTRange=2
SE.MaxNoPeakCluster=4
SE.MinFrag=10
SE.MinMSIntensity=1
SE.MinMSMSIntensity=1
SE.MinNoPeakCluster=2
SE.NoMissedScan=1
SE.SN=1.1
WindowSize=25
crystalc.run-crystalc=false
database.db-path=C\:\\Users\\srice\\Downloads\\FragPipe-14.0\\2021-02-24-decoys-reviewed-contam-UP000005640.fas
database.decoy-tag=rev_
diaumpire_se.params=
fragpipe-config.bin-msfragger=C\:\\Users\\srice\\Downloads\\FragPipe-14.0\\bin\\fragpipe\\bin\\MSFragger-3.1.1\\MSFragger-3.1.1.jar
fragpipe-config.bin-philosopher=C\:\\Users\\srice\\Downloads\\FragPipe-14.0\\fragpipe\\lib\\..\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\ProgramData\\Anaconda3\\python.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
ionquant.minions=1
ionquant.minisotopes=1
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=2
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.deisotope=0
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown=stricttrypsin
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-50
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=50
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=stricttrypsin
msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 57.021464,C (cysteine),true,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 0.000000,site_06,false,1; 0.000000,site_07,false,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mgf=true
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
path.textfield.msconvert=C\:\\Program Files (x86)\\ProteoWizard 3.0.18353 64-bit\\msconvert.exe
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=true
peptide-prophet.run-peptide-prophet=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --prot 0.01
phi-report.pep-level-summary=false
phi-report.print-decoys=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
ptmprophet.run-ptmprophet=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=0,203.07937,406.15874,568.21156,730.26438,892.3172,349.137279
ptmshepherd.diag_ions=204.086646,186.076086,168.065526,366.139466,144.0656,138.055,512.197375,292.1026925,274.0921325,657.2349,243.026426,405.079246,485.045576,308.09761
ptmshepherd.glyco_mode=true
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
ptmshepherd.localization_background=4
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.remainder_masses=203.07937
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=false
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.rt-cal=ciRT
speclibgen.easypqp.select-file.text=D\:\\blood.timsTOF\\pasef_CiRT_linear.txt
speclibgen.run-speclibgen=true
speclibgen.use-easypqp=true
speclibgen.use-spectrast=false
tmtintegrator.add_Ref=-1
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.groupby=0
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=C\:\\Users\\srice\\Downloads\\HeLa_Evosep_diaPASEF_RAW\\diaU
workflow.input.data-type.im-ms=true
workflow.input.data-type.regular-ms=false
workflow.process-exps-separately=false
workflow.ram=0
workflow.threads=7

UmpireSe java -jar C:\Users\srice\Downloads\FragPipe-14.0\fragpipe\lib..\tools\dia_umpire_se-2.1.5.jar C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.mzXML C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\umpire-se_2021-02-26_12-15-03.params

DIA-Umpire singal extraction analysis (version: v2.1.5) 2021-02-26 12:15:04,502 INFO [root] Version: v2.1.5 2021-02-26 12:15:04,503 INFO [root] Parameter file:C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\umpire-se_2021-02-26_12-15-03.params 2021-02-26 12:15:04,503 INFO [root] Spectra file:C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.mzXML 2021-02-26 12:15:04,509 INFO [root] 2021-02-26 12:15:04,509 INFO [root] #################################################################################################### 2021-02-26 12:15:04,510 INFO [root] #No of threads 2021-02-26 12:15:04,511 INFO [root] Thread = 4 2021-02-26 12:15:04,511 INFO [root] #################################################################################################### 2021-02-26 12:15:04,512 INFO [root] 2021-02-26 12:15:04,512 INFO [root] ## omit Thread 2021-02-26 12:15:04,512 INFO [root] 2021-02-26 12:15:04,512 INFO [root] #Precursor-fragments grouping parameters 2021-02-26 12:15:04,512 INFO [root] RPmax = 25 2021-02-26 12:15:04,512 INFO [root] RFmax = 500 2021-02-26 12:15:04,512 INFO [root] CorrThreshold = 0 2021-02-26 12:15:04,513 INFO [root] DeltaApex = 0.3 2021-02-26 12:15:04,514 INFO [root] RTOverlap = 0.3 2021-02-26 12:15:04,514 INFO [root] 2021-02-26 12:15:04,514 INFO [root] #Fragment intensity adjustments 2021-02-26 12:15:04,514 INFO [root] # change BoostComplementaryIon if later using database search results to build libraries for Skyline/OpenSWATH 2021-02-26 12:15:04,514 INFO [root] AdjustFragIntensity = true 2021-02-26 12:15:04,515 INFO [root] BoostComplementaryIon = false 2021-02-26 12:15:04,515 INFO [root] 2021-02-26 12:15:04,515 INFO [root] #Export detected MS1 features (output feature file can be loaded and mapped to RAW data in BatMass) 2021-02-26 12:15:04,515 INFO [root] ExportPrecursorPeak = false 2021-02-26 12:15:04,515 INFO [root] 2021-02-26 12:15:04,515 INFO [root] #Signal extraction: mass accuracy and resolution 2021-02-26 12:15:04,516 INFO [root] # resolution parameter matters only for data generated in profile mode 2021-02-26 12:15:04,516 INFO [root] SE.MS1PPM = 15 2021-02-26 12:15:04,516 INFO [root] SE.MS2PPM = 25 2021-02-26 12:15:04,516 INFO [root] SE.Resolution = 60000 2021-02-26 12:15:04,516 INFO [root] 2021-02-26 12:15:04,516 INFO [root] #Signal extraction: signal to noise filter 2021-02-26 12:15:04,516 INFO [root] SE.SN = 1.1 2021-02-26 12:15:04,516 INFO [root] SE.MS2SN = 1.1 2021-02-26 12:15:04,516 INFO [root] 2021-02-26 12:15:04,516 INFO [root] #Signal extraction: minimum signal intensity filter 2021-02-26 12:15:04,517 INFO [root] # for Thermo data, filtering is usually not necessary. Set SE.EstimateBG to false and SE.MinMSIntensity and SE.MinMSMSIntensity to a low value, e.g. 1 2021-02-26 12:15:04,517 INFO [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.EstimateBG to yes (or apply SE.MinMSIntensity and SE.MinMSMSIntensity values based on BatMass visualization) 2021-02-26 12:15:04,517 INFO [root] SE.EstimateBG = false 2021-02-26 12:15:04,517 INFO [root] SE.MinMSIntensity = 1 2021-02-26 12:15:04,517 INFO [root] SE.MinMSMSIntensity = 1 2021-02-26 12:15:04,517 INFO [root] 2021-02-26 12:15:04,517 INFO [root] #Signal extraction: peak curve detection and isotope grouping 2021-02-26 12:15:04,517 INFO [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.NoMissedScan to 1 2021-02-26 12:15:04,517 INFO [root] SE.NoMissedScan = 1 2021-02-26 12:15:04,517 INFO [root] SE.MaxCurveRTRange = 2 2021-02-26 12:15:04,518 INFO [root] SE.RemoveGroupedPeaks = true 2021-02-26 12:15:04,518 INFO [root] SE.RemoveGroupedPeaksRTOverlap = 0.3 2021-02-26 12:15:04,518 INFO [root] SE.RemoveGroupedPeaksCorr = 0.3 2021-02-26 12:15:04,518 INFO [root] SE.MinNoPeakCluster = 2 2021-02-26 12:15:04,518 INFO [root] SE.MaxNoPeakCluster = 4 2021-02-26 12:15:04,556 INFO [root] 2021-02-26 12:15:04,556 INFO [root] #Signal extraction: filtering of MS1 features 2021-02-26 12:15:04,556 INFO [root] # if interested in modified peptides, increase MassDefectOffset parameter, or set SE.MassDefectFilter to false 2021-02-26 12:15:04,556 INFO [root] SE.IsoPattern = 0.3 2021-02-26 12:15:04,557 INFO [root] SE.MassDefectFilter = true 2021-02-26 12:15:04,557 INFO [root] SE.MassDefectOffset = 0.1 2021-02-26 12:15:04,557 INFO [root] 2021-02-26 12:15:04,557 INFO [root] #Signal extraction: other 2021-02-26 12:15:04,557 INFO [root] SE.StartCharge = 1 2021-02-26 12:15:04,557 INFO [root] SE.EndCharge = 5 2021-02-26 12:15:04,557 INFO [root] SE.MS2StartCharge = 2 2021-02-26 12:15:04,557 INFO [root] SE.MS2EndCharge = 5 2021-02-26 12:15:04,558 INFO [root] SE.MinFrag = 10 2021-02-26 12:15:04,558 INFO [root] SE.StartRT = 0 2021-02-26 12:15:04,558 INFO [root] SE.EndRT = 9999 2021-02-26 12:15:04,558 INFO [root] SE.MinMZ = 200 2021-02-26 12:15:04,558 INFO [root] SE.MinPrecursorMass = 600 2021-02-26 12:15:04,558 INFO [root] SE.MaxPrecursorMass = 5000 2021-02-26 12:15:04,558 INFO [root] 2021-02-26 12:15:04,558 INFO [root] 2021-02-26 12:15:04,559 INFO [root] #Isolation window setting 2021-02-26 12:15:04,559 INFO [root] #The current version supports the following window type: SWATH (fixed window size), V_SWATH (variable SWATH window), MSX, MSE, pSMART 2021-02-26 12:15:04,559 INFO [root] WindowType = SWATH 2021-02-26 12:15:04,559 INFO [root] 2021-02-26 12:15:04,559 INFO [root] #Fix window size (For SWATH) 2021-02-26 12:15:04,559 INFO [root] # for Thermo data, this will be determined from raw data automatically 2021-02-26 12:15:04,559 INFO [root] WindowSize = 25 2021-02-26 12:15:04,559 INFO [root] 2021-02-26 12:15:04,559 INFO [root] #Variable SWATH window setting (start m/z, end m/z, separated by Tab) 2021-02-26 12:15:04,559 INFO [root] # for Thermo data, this will be determined from raw data automatically 2021-02-26 12:15:04,559 INFO [root] ==window setting begin 2021-02-26 12:15:04,559 INFO [root] 2021-02-26 12:15:04,560 INFO [root] ================================================================================================= 2021-02-26 12:15:04,560 INFO [root] Processing C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450.mzXML.... 2021-02-26 12:15:04,563 INFO [root] Writing DIA setting to file:C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_diasetting.ser... 2021-02-26 12:15:04,571 INFO [root] Writing parameter to file:C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_params.ser... 2021-02-26 12:15:04,577 INFO [root] Module A: Signal extraction WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by org.nustaq.serialization.FSTClazzInfo (file:/C:/Users/srice/Downloads/FragPipe-14.0/fragpipe/tools/dia_umpire_se-2.1.5.jar) to field java.lang.String.value WARNING: Please consider reporting this to the maintainers of org.nustaq.serialization.FSTClazzInfo WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release 2021-02-26 12:15:05,139 INFO [root] Writing DIA setting to file:C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\60SPD_py8\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_diasetting.ser... 2021-02-26 12:15:05,278 INFO [root] Processing MS1 peak detection 2021-02-26 12:15:05,280 INFO [root] MS1 average cycle time : 0.9559337 seconds 2021-02-26 12:15:06,337 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:15:06,337 INFO [root] Smoothing detected signals...... 2021-02-26 12:15:07,093 INFO [root] 27416 Peak curves found (Memory usage:26MB) 2021-02-26 12:15:07,093 INFO [root] Inclusion mz values found: 0/0 2021-02-26 12:15:07,093 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:15:07,094 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:15:07,410 INFO [root] No of ion clusters:2548 (Memory usage:20MB) 2021-02-26 12:15:07,414 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_PeakCluster.serFS... 2021-02-26 12:15:07,482 INFO [root] ================================================================================== 2021-02-26 12:15:07,483 INFO [root] Processing DIA MS2 (mz range):975.0_1000.0( 1/24 ) 2021-02-26 12:15:07,500 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:15:07,500 INFO [root] Smoothing detected signals...... 2021-02-26 12:15:10,603 INFO [root] 11716 Peak curves found (Memory usage:32MB) 2021-02-26 12:15:10,608 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:15:10,608 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:15:10,897 INFO [root] No of ion clusters:811 (Memory usage:33MB) 2021-02-26 12:15:10,898 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_975_1000_PeakCluster.serFS... 2021-02-26 12:15:10,916 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:15:10,916 INFO [root] No. of fragment peaks: 11782 2021-02-26 12:15:10,920 INFO [root] No. of remaining fragment peaks: 9459 2021-02-26 12:15:10,921 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:15:11,000 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:15:12,268 INFO [root] ================================================================================== 2021-02-26 12:15:12,269 INFO [root] Processing DIA MS2 (mz range):950.0_975.0( 2/24 ) 2021-02-26 12:15:12,283 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:15:12,284 INFO [root] Smoothing detected signals...... 2021-02-26 12:15:15,294 INFO [root] 12226 Peak curves found (Memory usage:33MB) 2021-02-26 12:15:15,297 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:15:15,297 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:15:15,488 INFO [root] No of ion clusters:880 (Memory usage:34MB) 2021-02-26 12:15:15,488 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_950_975_PeakCluster.serFS... 2021-02-26 12:15:15,501 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:15:15,501 INFO [root] No. of fragment peaks: 12285 2021-02-26 12:15:15,504 INFO [root] No. of remaining fragment peaks: 9894 2021-02-26 12:15:15,504 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:15:15,525 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:15:16,903 INFO [root] ================================================================================== 2021-02-26 12:15:16,903 INFO [root] Processing DIA MS2 (mz range):925.0_950.0( 3/24 ) 2021-02-26 12:15:16,915 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:15:16,915 INFO [root] Smoothing detected signals...... 2021-02-26 12:15:19,454 INFO [root] 12704 Peak curves found (Memory usage:33MB) 2021-02-26 12:15:19,457 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:15:19,457 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:15:19,676 INFO [root] No of ion clusters:931 (Memory usage:35MB) 2021-02-26 12:15:19,676 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_925_950_PeakCluster.serFS... 2021-02-26 12:15:19,688 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:15:19,688 INFO [root] No. of fragment peaks: 12769 2021-02-26 12:15:19,691 INFO [root] No. of remaining fragment peaks: 10519 2021-02-26 12:15:19,691 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:15:19,707 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:15:20,952 INFO [root] ================================================================================== 2021-02-26 12:15:20,952 INFO [root] Processing DIA MS2 (mz range):900.0_925.0( 4/24 ) 2021-02-26 12:15:20,966 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:15:20,966 INFO [root] Smoothing detected signals...... 2021-02-26 12:15:23,721 INFO [root] 12248 Peak curves found (Memory usage:33MB) 2021-02-26 12:15:23,723 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:15:23,723 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:15:23,918 INFO [root] No of ion clusters:1008 (Memory usage:35MB) 2021-02-26 12:15:23,918 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_900_925_PeakCluster.serFS... 2021-02-26 12:15:23,932 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:15:23,932 INFO [root] No. of fragment peaks: 12313 2021-02-26 12:15:23,935 INFO [root] No. of remaining fragment peaks: 10257 2021-02-26 12:15:23,935 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:15:23,962 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:15:25,386 INFO [root] ================================================================================== 2021-02-26 12:15:25,386 INFO [root] Processing DIA MS2 (mz range):875.0_900.0( 5/24 ) 2021-02-26 12:15:25,400 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:15:25,400 INFO [root] Smoothing detected signals...... 2021-02-26 12:15:27,940 INFO [root] 12724 Peak curves found (Memory usage:34MB) 2021-02-26 12:15:27,942 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:15:27,942 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:15:28,167 INFO [root] No of ion clusters:1188 (Memory usage:35MB) 2021-02-26 12:15:28,167 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_875_900_PeakCluster.serFS... 2021-02-26 12:15:28,182 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:15:28,182 INFO [root] No. of fragment peaks: 12765 2021-02-26 12:15:28,184 INFO [root] No. of remaining fragment peaks: 10343 2021-02-26 12:15:28,184 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:15:28,215 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:15:29,908 INFO [root] ================================================================================== 2021-02-26 12:15:29,908 INFO [root] Processing DIA MS2 (mz range):850.0_875.0( 6/24 ) 2021-02-26 12:15:29,921 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:15:29,921 INFO [root] Smoothing detected signals...... 2021-02-26 12:15:32,444 INFO [root] 12983 Peak curves found (Memory usage:34MB) 2021-02-26 12:15:32,447 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:15:32,447 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:15:32,671 INFO [root] No of ion clusters:1229 (Memory usage:37MB) 2021-02-26 12:15:32,672 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_850_875_PeakCluster.serFS... 2021-02-26 12:15:32,690 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:15:32,690 INFO [root] No. of fragment peaks: 13016 2021-02-26 12:15:32,692 INFO [root] No. of remaining fragment peaks: 10683 2021-02-26 12:15:32,692 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:15:32,707 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:15:34,428 INFO [root] ================================================================================== 2021-02-26 12:15:34,428 INFO [root] Processing DIA MS2 (mz range):825.0_850.0( 7/24 ) 2021-02-26 12:15:34,439 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:15:34,439 INFO [root] Smoothing detected signals...... 2021-02-26 12:15:36,870 INFO [root] 13433 Peak curves found (Memory usage:34MB) 2021-02-26 12:15:36,872 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:15:36,872 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:15:37,079 INFO [root] No of ion clusters:1242 (Memory usage:36MB) 2021-02-26 12:15:37,079 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_825_850_PeakCluster.serFS... 2021-02-26 12:15:37,097 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:15:37,097 INFO [root] No. of fragment peaks: 13470 2021-02-26 12:15:37,099 INFO [root] No. of remaining fragment peaks: 11263 2021-02-26 12:15:37,099 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:15:37,118 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:15:38,923 INFO [root] ================================================================================== 2021-02-26 12:15:38,923 INFO [root] Processing DIA MS2 (mz range):800.0_825.0( 8/24 ) 2021-02-26 12:15:38,935 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:15:38,935 INFO [root] Smoothing detected signals...... 2021-02-26 12:15:41,338 INFO [root] 13562 Peak curves found (Memory usage:38MB) 2021-02-26 12:15:41,340 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:15:41,340 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:15:41,547 INFO [root] No of ion clusters:1237 (Memory usage:40MB) 2021-02-26 12:15:41,547 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_800_825_PeakCluster.serFS... 2021-02-26 12:15:41,563 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:15:41,563 INFO [root] No. of fragment peaks: 13600 2021-02-26 12:15:41,565 INFO [root] No. of remaining fragment peaks: 11245 2021-02-26 12:15:41,565 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:15:41,590 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:15:43,380 INFO [root] ================================================================================== 2021-02-26 12:15:43,380 INFO [root] Processing DIA MS2 (mz range):775.0_800.0( 9/24 ) 2021-02-26 12:15:43,391 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:15:43,391 INFO [root] Smoothing detected signals...... 2021-02-26 12:15:45,948 INFO [root] 14545 Peak curves found (Memory usage:39MB) 2021-02-26 12:15:45,950 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:15:45,950 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:15:46,242 INFO [root] No of ion clusters:1718 (Memory usage:41MB) 2021-02-26 12:15:46,243 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_775_800_PeakCluster.serFS... 2021-02-26 12:15:46,266 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:15:46,266 INFO [root] No. of fragment peaks: 14580 2021-02-26 12:15:46,268 INFO [root] No. of remaining fragment peaks: 12340 2021-02-26 12:15:46,268 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:15:46,295 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:15:48,934 INFO [root] ================================================================================== 2021-02-26 12:15:48,934 INFO [root] Processing DIA MS2 (mz range):750.0_775.0( 10/24 ) 2021-02-26 12:15:48,946 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:15:48,946 INFO [root] Smoothing detected signals...... 2021-02-26 12:15:51,682 INFO [root] 14582 Peak curves found (Memory usage:39MB) 2021-02-26 12:15:51,685 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:15:51,685 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:15:51,936 INFO [root] No of ion clusters:1652 (Memory usage:42MB) 2021-02-26 12:15:51,937 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_750_775_PeakCluster.serFS... 2021-02-26 12:15:51,958 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:15:51,958 INFO [root] No. of fragment peaks: 14624 2021-02-26 12:15:51,960 INFO [root] No. of remaining fragment peaks: 12570 2021-02-26 12:15:51,960 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:15:51,988 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:15:54,632 INFO [root] ================================================================================== 2021-02-26 12:15:54,632 INFO [root] Processing DIA MS2 (mz range):725.0_750.0( 11/24 ) 2021-02-26 12:15:54,643 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:15:54,643 INFO [root] Smoothing detected signals...... 2021-02-26 12:15:56,915 INFO [root] 15499 Peak curves found (Memory usage:40MB) 2021-02-26 12:15:56,918 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:15:56,918 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:15:57,198 INFO [root] No of ion clusters:1729 (Memory usage:43MB) 2021-02-26 12:15:57,198 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_725_750_PeakCluster.serFS... 2021-02-26 12:15:57,220 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:15:57,220 INFO [root] No. of fragment peaks: 15516 2021-02-26 12:15:57,222 INFO [root] No. of remaining fragment peaks: 13254 2021-02-26 12:15:57,222 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:15:57,244 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:15:59,805 INFO [root] ================================================================================== 2021-02-26 12:15:59,806 INFO [root] Processing DIA MS2 (mz range):700.0_725.0( 12/24 ) 2021-02-26 12:15:59,816 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:15:59,816 INFO [root] Smoothing detected signals...... 2021-02-26 12:16:02,064 INFO [root] 15610 Peak curves found (Memory usage:40MB) 2021-02-26 12:16:02,066 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:16:02,066 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:16:02,337 INFO [root] No of ion clusters:1650 (Memory usage:43MB) 2021-02-26 12:16:02,337 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_700_725_PeakCluster.serFS... 2021-02-26 12:16:02,359 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:16:02,359 INFO [root] No. of fragment peaks: 15635 2021-02-26 12:16:02,361 INFO [root] No. of remaining fragment peaks: 13444 2021-02-26 12:16:02,361 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:16:02,393 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:16:05,179 INFO [root] ================================================================================== 2021-02-26 12:16:05,179 INFO [root] Processing DIA MS2 (mz range):675.0_700.0( 13/24 ) 2021-02-26 12:16:05,188 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:16:05,188 INFO [root] Smoothing detected signals...... 2021-02-26 12:16:07,384 INFO [root] 16317 Peak curves found (Memory usage:41MB) 2021-02-26 12:16:07,385 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:16:07,385 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:16:07,604 INFO [root] No of ion clusters:1619 (Memory usage:43MB) 2021-02-26 12:16:07,604 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_675_700_PeakCluster.serFS... 2021-02-26 12:16:07,625 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:16:07,625 INFO [root] No. of fragment peaks: 16330 2021-02-26 12:16:07,627 INFO [root] No. of remaining fragment peaks: 14007 2021-02-26 12:16:07,627 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:16:07,658 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:16:10,075 INFO [root] ================================================================================== 2021-02-26 12:16:10,076 INFO [root] Processing DIA MS2 (mz range):650.0_675.0( 14/24 ) 2021-02-26 12:16:10,085 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:16:10,085 INFO [root] Smoothing detected signals...... 2021-02-26 12:16:12,186 INFO [root] 16043 Peak curves found (Memory usage:41MB) 2021-02-26 12:16:12,188 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:16:12,188 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:16:12,381 INFO [root] No of ion clusters:1511 (Memory usage:43MB) 2021-02-26 12:16:12,381 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_650_675_PeakCluster.serFS... 2021-02-26 12:16:12,399 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:16:12,399 INFO [root] No. of fragment peaks: 16060 2021-02-26 12:16:12,401 INFO [root] No. of remaining fragment peaks: 13888 2021-02-26 12:16:12,401 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:16:12,440 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:16:14,775 INFO [root] ================================================================================== 2021-02-26 12:16:14,776 INFO [root] Processing DIA MS2 (mz range):625.0_650.0( 15/24 ) 2021-02-26 12:16:14,785 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:16:14,785 INFO [root] Smoothing detected signals...... 2021-02-26 12:16:16,976 INFO [root] 16727 Peak curves found (Memory usage:42MB) 2021-02-26 12:16:16,978 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:16:16,978 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:16:17,167 INFO [root] No of ion clusters:1448 (Memory usage:44MB) 2021-02-26 12:16:17,168 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_625_650_PeakCluster.serFS... 2021-02-26 12:16:17,186 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:16:17,186 INFO [root] No. of fragment peaks: 16738 2021-02-26 12:16:17,188 INFO [root] No. of remaining fragment peaks: 14510 2021-02-26 12:16:17,188 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:16:17,222 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:16:19,538 INFO [root] ================================================================================== 2021-02-26 12:16:19,538 INFO [root] Processing DIA MS2 (mz range):600.0_625.0( 16/24 ) 2021-02-26 12:16:19,548 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:16:19,548 INFO [root] Smoothing detected signals...... 2021-02-26 12:16:21,962 INFO [root] 17138 Peak curves found (Memory usage:42MB) 2021-02-26 12:16:21,964 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:16:21,964 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:16:22,137 INFO [root] No of ion clusters:1351 (Memory usage:44MB) 2021-02-26 12:16:22,137 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_600_625_PeakCluster.serFS... 2021-02-26 12:16:22,154 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:16:22,154 INFO [root] No. of fragment peaks: 17147 2021-02-26 12:16:22,156 INFO [root] No. of remaining fragment peaks: 15053 2021-02-26 12:16:22,156 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:16:22,195 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:16:24,400 INFO [root] ================================================================================== 2021-02-26 12:16:24,400 INFO [root] Processing DIA MS2 (mz range):575.0_600.0( 17/24 ) 2021-02-26 12:16:24,410 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:16:24,410 INFO [root] Smoothing detected signals...... 2021-02-26 12:16:26,775 INFO [root] 17178 Peak curves found (Memory usage:42MB) 2021-02-26 12:16:26,777 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:16:26,777 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:16:26,921 INFO [root] No of ion clusters:1212 (Memory usage:45MB) 2021-02-26 12:16:26,921 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_575_600_PeakCluster.serFS... 2021-02-26 12:16:26,936 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:16:26,936 INFO [root] No. of fragment peaks: 17190 2021-02-26 12:16:26,938 INFO [root] No. of remaining fragment peaks: 14939 2021-02-26 12:16:26,938 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:16:26,991 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:16:28,895 INFO [root] ================================================================================== 2021-02-26 12:16:28,896 INFO [root] Processing DIA MS2 (mz range):550.0_575.0( 18/24 ) 2021-02-26 12:16:28,905 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:16:28,905 INFO [root] Smoothing detected signals...... 2021-02-26 12:16:31,198 INFO [root] 18276 Peak curves found (Memory usage:43MB) 2021-02-26 12:16:31,200 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:16:31,200 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:16:31,332 INFO [root] No of ion clusters:1046 (Memory usage:46MB) 2021-02-26 12:16:31,332 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_550_575_PeakCluster.serFS... 2021-02-26 12:16:31,345 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:16:31,345 INFO [root] No. of fragment peaks: 18284 2021-02-26 12:16:31,347 INFO [root] No. of remaining fragment peaks: 15978 2021-02-26 12:16:31,347 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:16:31,384 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:16:33,048 INFO [root] ================================================================================== 2021-02-26 12:16:33,048 INFO [root] Processing DIA MS2 (mz range):525.0_550.0( 19/24 ) 2021-02-26 12:16:33,057 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:16:33,057 INFO [root] Smoothing detected signals...... 2021-02-26 12:16:35,284 INFO [root] 19009 Peak curves found (Memory usage:44MB) 2021-02-26 12:16:35,285 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:16:35,286 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:16:35,404 INFO [root] No of ion clusters:945 (Memory usage:46MB) 2021-02-26 12:16:35,404 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_525_550_PeakCluster.serFS... 2021-02-26 12:16:35,417 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:16:35,417 INFO [root] No. of fragment peaks: 19013 2021-02-26 12:16:35,419 INFO [root] No. of remaining fragment peaks: 16663 2021-02-26 12:16:35,419 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:16:35,453 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:16:37,089 INFO [root] ================================================================================== 2021-02-26 12:16:37,089 INFO [root] Processing DIA MS2 (mz range):500.0_525.0( 20/24 ) 2021-02-26 12:16:37,097 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:16:37,097 INFO [root] Smoothing detected signals...... 2021-02-26 12:16:39,523 INFO [root] 19367 Peak curves found (Memory usage:45MB) 2021-02-26 12:16:39,525 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:16:39,525 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:16:39,613 INFO [root] No of ion clusters:721 (Memory usage:47MB) 2021-02-26 12:16:39,613 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_500_525_PeakCluster.serFS... 2021-02-26 12:16:39,623 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:16:39,623 INFO [root] No. of fragment peaks: 19375 2021-02-26 12:16:39,625 INFO [root] No. of remaining fragment peaks: 16964 2021-02-26 12:16:39,625 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:16:39,669 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:16:40,935 INFO [root] ================================================================================== 2021-02-26 12:16:40,935 INFO [root] Processing DIA MS2 (mz range):475.0_500.0( 21/24 ) 2021-02-26 12:16:40,944 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:16:40,944 INFO [root] Smoothing detected signals...... 2021-02-26 12:16:43,302 INFO [root] 19372 Peak curves found (Memory usage:42MB) 2021-02-26 12:16:43,303 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:16:43,303 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:16:43,386 INFO [root] No of ion clusters:592 (Memory usage:44MB) 2021-02-26 12:16:43,386 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_475_500_PeakCluster.serFS... 2021-02-26 12:16:43,396 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:16:43,396 INFO [root] No. of fragment peaks: 19373 2021-02-26 12:16:43,398 INFO [root] No. of remaining fragment peaks: 16787 2021-02-26 12:16:43,398 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:16:43,436 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:16:44,546 INFO [root] ================================================================================== 2021-02-26 12:16:44,546 INFO [root] Processing DIA MS2 (mz range):450.0_475.0( 22/24 ) 2021-02-26 12:16:44,555 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:16:44,555 INFO [root] Smoothing detected signals...... 2021-02-26 12:16:47,057 INFO [root] 19897 Peak curves found (Memory usage:42MB) 2021-02-26 12:16:47,059 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:16:47,059 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:16:47,128 INFO [root] No of ion clusters:439 (Memory usage:44MB) 2021-02-26 12:16:47,128 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_450_475_PeakCluster.serFS... 2021-02-26 12:16:47,134 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:16:47,134 INFO [root] No. of fragment peaks: 19903 2021-02-26 12:16:47,136 INFO [root] No. of remaining fragment peaks: 17180 2021-02-26 12:16:47,136 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:16:47,173 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:16:48,029 INFO [root] ================================================================================== 2021-02-26 12:16:48,029 INFO [root] Processing DIA MS2 (mz range):425.0_450.0( 23/24 ) 2021-02-26 12:16:48,038 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:16:48,038 INFO [root] Smoothing detected signals...... 2021-02-26 12:16:50,626 INFO [root] 20479 Peak curves found (Memory usage:43MB) 2021-02-26 12:16:50,627 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:16:50,627 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:16:50,700 INFO [root] No of ion clusters:423 (Memory usage:45MB) 2021-02-26 12:16:50,700 INFO [root] Writing PeakCluster serialization to file:20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_425_450_PeakCluster.serFS... 2021-02-26 12:16:50,707 INFO [root] Performing mass defect filter on fragment peaks 2021-02-26 12:16:50,707 INFO [root] No. of fragment peaks: 20486 2021-02-26 12:16:50,709 INFO [root] No. of remaining fragment peaks: 17633 2021-02-26 12:16:50,709 INFO [root] Building precursor-fragment pairs for MS1 features.... 2021-02-26 12:16:50,735 INFO [root] Building precursor-fragment pairs for unfragmented ions.... 2021-02-26 12:16:51,574 INFO [root] ================================================================================== 2021-02-26 12:16:51,574 INFO [root] Processing DIA MS2 (mz range):400.0_425.0( 24/24 ) 2021-02-26 12:16:51,584 INFO [root] Processing all scans to detect possible m/z peak curves and 2021-02-26 12:16:51,584 INFO [root] Smoothing detected signals...... 2021-02-26 12:16:54,122 INFO [root] 21502 Peak curves found (Memory usage:44MB) 2021-02-26 12:16:54,123 INFO [root] Grouping isotopic peak curves........ 2021-02-26 12:16:54,123 INFO [root] Building PeakCurve Mass-RT KD tree 2021-02-26 12:16:54,178 INFO [root] No of ion clusters:250 (Memory usage:46MB) 2021-02-26 1

fcyu commented 3 years ago

The log file was truncated by GitHub. Can you zip it and attach it? But I have a question: is your data from diaPASEF since your folder name is HeLa_Evosep_diaPASEF_RAW?

Best,

Fengchao

sjr24 commented 3 years ago

Yes, it is diaPASEF.

From: Fengchao [mailto:notifications@github.com] Sent: Friday, February 26, 2021 12:48 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Rice, Shawn srice@pennstatehealth.psu.edu; Author author@noreply.github.com Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

Attention: This email originated outside of Penn State Health. Use caution when clicking links or opening attachments.

The log file was truncated by GitHub. Can you zip it and attach it? But I have a question: is your data from diaPASEF since your folder name is HeLa_Evosep_diaPASEF_RAW?

Best,

Fengchao

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fcyu commented 3 years ago

OK. DIA-Umpire does not support diaPASEF.

Best,

Fengchao

sjr24 commented 3 years ago

Zipped file is attached. Is the workflow not compatible with diaPASEF?

From: Fengchao [mailto:notifications@github.com] Sent: Friday, February 26, 2021 12:48 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Rice, Shawn srice@pennstatehealth.psu.edu; Author author@noreply.github.com Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

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The log file was truncated by GitHub. Can you zip it and attach it? But I have a question: is your data from diaPASEF since your folder name is HeLa_Evosep_diaPASEF_RAW?

Best,

Fengchao

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fcyu commented 3 years ago

Correct, the workflow is not compatible with diaPASEF.

Best,

Fengchao

sjr24 commented 3 years ago

Thanks for the information.

From: Fengchao [mailto:notifications@github.com] Sent: Friday, February 26, 2021 12:52 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Rice, Shawn srice@pennstatehealth.psu.edu; Author author@noreply.github.com Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

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OK. DIA-Umpire does not support diaPASEF.

Best,

Fengchao

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fcyu commented 3 years ago

You are welcome.

Best,

Fengchao

fcyu commented 3 years ago

Sorry that I cannot find the zip file. Can you send them to yufe@umich.edu?

Thanks,

Fengchao

sjr24 commented 3 years ago

Sorry, I left the lab. I’ll send it later this evening.

Thanks, Shawn

From: Fengchao notifications@github.com Date: February 26, 2021 at 5:10:49 PM EST To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Rice, Shawn srice@pennstatehealth.psu.edu, Author author@noreply.github.com Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

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Sorry that I cannot find the zip file. Can you send them to yufe@umich.edumailto:yufe@umich.edu?

Thanks,

Fengchao

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guoci commented 3 years ago

@sjr24 can you also send

C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_uncalibrated.mgf
C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_uncalibrated.mgf

sjr24 commented 3 years ago

I am using data from Meier et al. 2020 (diaPASEF keyword) downloaded from pride db. If you can not find I can send.

Thanks, Shawn

From: guoci notifications@github.com Date: February 27, 2021 at 5:14:27 PM EST To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Rice, Shawn srice@pennstatehealth.psu.edu, Mention mention@noreply.github.com Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

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C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_uncalibrated.mgf C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_uncalibrated.mgf

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anesvi commented 3 years ago

We have that data, but not able to get the same error.

Sjr24, how did you convert the data? When I tested with DIA-Umpire, I got better results than what I see in your log file. I think you converted with a very aggressive peak filtering or something. At any rate, we are not “officially” supporting diaPASEF with DIA-Umpire at this point because it does not take IM (so suboptimal performance), although it works.

Best Alexey

From: sjr24 notifications@github.com Sent: Saturday, February 27, 2021 6:46 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

External Email - Use Caution I am using data from Meier et al. 2020 (diaPASEF keyword) downloaded from pride db. If you can not find I can send.

Thanks, Shawn

From: guoci notifications@github.com<mailto:notifications@github.com> Date: February 27, 2021 at 5:14:27 PM EST To: Nesvilab/FragPipe FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com> Cc: Rice, Shawn srice@pennstatehealth.psu.edu<mailto:srice@pennstatehealth.psu.edu>, Mention mention@noreply.github.com<mailto:mention@noreply.github.com> Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

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C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_uncalibrated.mgf C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_uncalibrated.mgf

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sjr24 commented 3 years ago

Alexey,

Greetings. I used ProteoWizard to convert the files. Could you send me instructions on how you converted the files and how you ran the files with DIA-U? I can see if it works for me.

Thanks, Shawn

From: Alexey Nesvizhskii [mailto:notifications@github.com] Sent: Saturday, February 27, 2021 6:53 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Rice, Shawn srice@pennstatehealth.psu.edu; Mention mention@noreply.github.com Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

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We have that data, but not able to get the same error.

Sjr24, how did you convert the data? When I tested with DIA-Umpire, I got better results than what I see in your log file. I think you converted with a very aggressive peak filtering or something. At any rate, we are not “officially” supporting diaPASEF with DIA-Umpire at this point because it does not take IM (so suboptimal performance), although it works.

Best Alexey

From: sjr24 notifications@github.com<mailto:notifications@github.com> Sent: Saturday, February 27, 2021 6:46 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com> Cc: Subscribed subscribed@noreply.github.com<mailto:subscribed@noreply.github.com> Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

External Email - Use Caution I am using data from Meier et al. 2020 (diaPASEF keyword) downloaded from pride db. If you can not find I can send.

Thanks, Shawn

From: guoci notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>> Date: February 27, 2021 at 5:14:27 PM EST To: Nesvilab/FragPipe FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com%3cmailto:FragPipe@noreply.github.com>> Cc: Rice, Shawn srice@pennstatehealth.psu.edu<mailto:srice@pennstatehealth.psu.edu<mailto:srice@pennstatehealth.psu.edu%3cmailto:srice@pennstatehealth.psu.edu>>, Mention mention@noreply.github.com<mailto:mention@noreply.github.com<mailto:mention@noreply.github.com%3cmailto:mention@noreply.github.com>> Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

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@sjr24<https://urldefense.com/v3/__https://github.com/sjr24__;!!Ls64Rlj6!itxfHmnCDvTZnhAgVPRbD7gjNeCmIRLf096Ks_e-Ao7a7AN8ooyZy7SFFFHblHCjczQ9dQ$%3Chttps://urldefense.com/v3/__https:/github.com/sjr24__;!!Ls64Rlj6!itxfHmnCDvTZnhAgVPRbD7gjNeCmIRLf096Ks_e-Ao7a7AN8ooyZy7SFFFHblHCjczQ9dQ$%3E%3E can you also send

C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_uncalibrated.mgf C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_uncalibrated.mgf

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anesvi commented 3 years ago

I don’t think I can send a screenshot of my Proteowizard settings via github. But I just selected mzXML, and checkbox ‘sum ion mobility scans’. Vendor peak picking was specified as usual.

In DIA-Umpire, use Max missed Scan= 1, AutomaticBG=yes, MS1 and MS2 SN set to 2.

If need more help here, contact by email, as this is a bit untested territory at this point.

Best Alexey

From: sjr24 notifications@github.com Sent: Saturday, February 27, 2021 11:52 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Nesvizhskii, Alexey nesvi@med.umich.edu; Comment comment@noreply.github.com Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

External Email - Use Caution Alexey,

Greetings. I used ProteoWizard to convert the files. Could you send me instructions on how you converted the files and how you ran the files with DIA-U? I can see if it works for me.

Thanks, Shawn

From: Alexey Nesvizhskii [mailto:notifications@github.com] Sent: Saturday, February 27, 2021 6:53 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com> Cc: Rice, Shawn srice@pennstatehealth.psu.edu<mailto:srice@pennstatehealth.psu.edu>; Mention mention@noreply.github.com<mailto:mention@noreply.github.com> Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

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We have that data, but not able to get the same error.

Sjr24, how did you convert the data? When I tested with DIA-Umpire, I got better results than what I see in your log file. I think you converted with a very aggressive peak filtering or something. At any rate, we are not “officially” supporting diaPASEF with DIA-Umpire at this point because it does not take IM (so suboptimal performance), although it works.

Best Alexey

From: sjr24 notifications@github.com<mailto:notifications@github.com<mailto:notifications@github.com%3cmailto:notifications@github.com>> Sent: Saturday, February 27, 2021 6:46 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com%3cmailto:FragPipe@noreply.github.com>> Cc: Subscribed subscribed@noreply.github.com<mailto:subscribed@noreply.github.com<mailto:subscribed@noreply.github.com%3cmailto:subscribed@noreply.github.com>> Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

External Email - Use Caution I am using data from Meier et al. 2020 (diaPASEF keyword) downloaded from pride db. If you can not find I can send.

Thanks, Shawn

Attention: This email originated outside of Penn State Health. Use caution when clicking links or opening attachments.

@sjr24<https://urldefense.com/v3/__https://github.com/sjr24__;!!Ls64Rlj6!itxfHmnCDvTZnhAgVPRbD7gjNeCmIRLf096Ks_e-Ao7a7AN8ooyZy7SFFFHblHCjczQ9dQ$%3Chttps://urldefense.com/v3/__https:/github.com/sjr24__;!!Ls64Rlj6!itxfHmnCDvTZnhAgVPRbD7gjNeCmIRLf096Ks_e-Ao7a7AN8ooyZy7SFFFHblHCjczQ9dQ$%3E%3E can you also send

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sjr24 commented 3 years ago

Thanks Alexey, it worked. There was an issue with building a library using fragpipe since the Q2 file failed calibration. The uncalibrated .mgf file was not able to be used. A library was able to be generated when I manually ran easypqp with the Q1 and Q2 files.

Thanks, Shawn

From: Alexey Nesvizhskii [mailto:notifications@github.com] Sent: Monday, March 1, 2021 10:56 AM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Rice, Shawn srice@pennstatehealth.psu.edu; Mention mention@noreply.github.com Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

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I don’t think I can send a screenshot of my Proteowizard settings via github. But I just selected mzXML, and checkbox ‘sum ion mobility scans’. Vendor peak picking was specified as usual.

In DIA-Umpire, use Max missed Scan= 1, AutomaticBG=yes, MS1 and MS2 SN set to 2.

If need more help here, contact by email, as this is a bit untested territory at this point.

Best Alexey

From: sjr24 notifications@github.com<mailto:notifications@github.com> Sent: Saturday, February 27, 2021 11:52 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com> Cc: Nesvizhskii, Alexey nesvi@med.umich.edu<mailto:nesvi@med.umich.edu>; Comment comment@noreply.github.com<mailto:comment@noreply.github.com> Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

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Greetings. I used ProteoWizard to convert the files. Could you send me instructions on how you converted the files and how you ran the files with DIA-U? I can see if it works for me.

Thanks, Shawn

From: Alexey Nesvizhskii [mailto:notifications@github.com] Sent: Saturday, February 27, 2021 6:53 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com%3cmailto:FragPipe@noreply.github.com>> Cc: Rice, Shawn srice@pennstatehealth.psu.edu<mailto:srice@pennstatehealth.psu.edu<mailto:srice@pennstatehealth.psu.edu%3cmailto:srice@pennstatehealth.psu.edu>>; Mention mention@noreply.github.com<mailto:mention@noreply.github.com<mailto:mention@noreply.github.com%3cmailto:mention@noreply.github.com>> Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

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We have that data, but not able to get the same error.

Sjr24, how did you convert the data? When I tested with DIA-Umpire, I got better results than what I see in your log file. I think you converted with a very aggressive peak filtering or something. At any rate, we are not “officially” supporting diaPASEF with DIA-Umpire at this point because it does not take IM (so suboptimal performance), although it works.

Best Alexey

External Email - Use Caution I am using data from Meier et al. 2020 (diaPASEF keyword) downloaded from pride db. If you can not find I can send.

Thanks, Shawn

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anesvi commented 3 years ago

I will ask Gui Ci to add a check in FragPipe. But as I said, DIA-Umpire for DiaPASEF need to be extended to read IM and use it to constrain peak tracing. If people convince me there is a need for that, we can do it... just a question of resources/priorities at this point. Alexey

Sent from my iPhone

On Mar 2, 2021, at 9:08 AM, sjr24 notifications@github.com wrote:

External Email - Use Caution

Thanks Alexey, it worked. There was an issue with building a library using fragpipe since the Q2 file failed calibration. The uncalibrated .mgf file was not able to be used. A library was able to be generated when I manually ran easypqp with the Q1 and Q2 files.

Thanks, Shawn

From: Alexey Nesvizhskii [mailto:notifications@github.com] Sent: Monday, March 1, 2021 10:56 AM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Rice, Shawn srice@pennstatehealth.psu.edu; Mention mention@noreply.github.com Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

Attention: This email originated outside of Penn State Health. Use caution when clicking links or opening attachments.

I don’t think I can send a screenshot of my Proteowizard settings via github. But I just selected mzXML, and checkbox ‘sum ion mobility scans’. Vendor peak picking was specified as usual.

In DIA-Umpire, use Max missed Scan= 1, AutomaticBG=yes, MS1 and MS2 SN set to 2.

If need more help here, contact by email, as this is a bit untested territory at this point.

Best Alexey

From: sjr24 notifications@github.com<mailto:notifications@github.com> Sent: Saturday, February 27, 2021 11:52 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com> Cc: Nesvizhskii, Alexey nesvi@med.umich.edu<mailto:nesvi@med.umich.edu>; Comment comment@noreply.github.com<mailto:comment@noreply.github.com> Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

External Email - Use Caution Alexey,

Greetings. I used ProteoWizard to convert the files. Could you send me instructions on how you converted the files and how you ran the files with DIA-U? I can see if it works for me.

Thanks, Shawn

From: Alexey Nesvizhskii [mailto:notifications@github.com] Sent: Saturday, February 27, 2021 6:53 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com<mailto:FragPipe@noreply.github.com%3cmailto:FragPipe@noreply.github.com>> Cc: Rice, Shawn srice@pennstatehealth.psu.edu<mailto:srice@pennstatehealth.psu.edu<mailto:srice@pennstatehealth.psu.edu%3cmailto:srice@pennstatehealth.psu.edu>>; Mention mention@noreply.github.com<mailto:mention@noreply.github.com<mailto:mention@noreply.github.com%3cmailto:mention@noreply.github.com>> Subject: Re: [Nesvilab/FragPipe] Easypqp error when making library from DIA-Umpire SE track using FragPipe (#311)

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We have that data, but not able to get the same error.

Sjr24, how did you convert the data? When I tested with DIA-Umpire, I got better results than what I see in your log file. I think you converted with a very aggressive peak filtering or something. At any rate, we are not “officially” supporting diaPASEF with DIA-Umpire at this point because it does not take IM (so suboptimal performance), although it works.

Best Alexey

External Email - Use Caution I am using data from Meier et al. 2020 (diaPASEF keyword) downloaded from pride db. If you can not find I can send.

Thanks, Shawn

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@sjr24<https://urldefense.com/v3/__https://github.com/sjr24__;!!Ls64Rlj6!itxfHmnCDvTZnhAgVPRbD7gjNeCmIRLf096Ks_e-Ao7a7AN8ooyZy7SFFFHblHCjczQ9dQ$%3Chttps://urldefense.com/v3/__https:/github.com/sjr24__;!!Ls64Rlj6!itxfHmnCDvTZnhAgVPRbD7gjNeCmIRLf096Ks_e-Ao7a7AN8ooyZy7SFFFHblHCjczQ9dQ$%3E%3E can you also send

C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q1_uncalibrated.mgf C:\Users\srice\Downloads\HeLa_Evosep_diaPASEF_RAW\diaU\20200428_Evosep_60SPD_SG06-16_MLHeLa_200ng_py8_S3-A4_1_2450_Q2_uncalibrated.mgf

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Nesvilab / FragPipe

Easypqp error when making library from DIA-Umpire SE track using FragPipe #311