pParse2.0 issue on loading timsTOF data

[fwelker]

pParsePlusLog.txt

Based on the online documentation I believe that pFind 3.2.3 should be able to analyse Bruker timsTOF data. I managed to load two .d folders (MS Data Format set to "TIMS" and MS Instrument automatically and exclusively set to "CID-TOF", then selected a range of normal parameters for the kind of dataset and search we would like to conduct.

pFind terminates after a few seconds with an error "[pFind] ALERT: Invalid_msmspath1_Path: ".

I attach the pParsePlusLog.txt file, as well as a copy of the error message I obtain in the Output panel of the pFind GUI below. Any suggestions on how to avoid this error going forward?

v==== pFind error message in Output panel ====v

[C:\Users\Users\Documents\Reindeer1\ : start from Data Extraction]

[pParse2Plus] "C:\Users\Users\Documents\Reindeer1\param\pFind.cfg" " -t -5 -z 5 -i 1 -C 1 -b 0 -m 0 -a 0 -p 1 -S 1 -P 1 " " -path:pParse2 ..\pParse.exe -Plus:pXtract_n_isotope 0 -path:fpath_pcfg_mode 2"
[pParse2Plus] 0, cfg_plus_args: {'path': {'pParse2': '..\pParse.exe', 'fpath_pcfg_mode': 2}, 'Plus': {'pXtract_n_isotope': 0}}
[pParse2Plus] 0, C:\Users\Users\Documents\20250527_PRI_TIMS7_EVO2_DDA_60SPD_8cmPS_P410_R1660_X2867_FWG000014_S124_S2-E4_1_12404.d
[cur] 2026-03-02 16:50:20 Starting...
[pParse2Plus] 0, Extract using pParse
[pParse2Plus] "C:\pFindStudio\pFind3\bin\pParse.exe" -D "C:\Users\Users\Documents\20250527_PRI_TIMS7_EVO2_DDA_60SPD_8cmPS_P410_R1660_X2867_FWG000014_S124_S2-E4_1_12404.d" -t -5 -z 5 -i 1 -C 1 -a 0 -p 1 -S 1 -b 0 -m 0 -P 1 -O "C:\Users\Users\Documents"

  *********************************************
 /       pParse2.0 (x64) from pFind Studio     \
/        Email  :  pfind@ict.ac.cn              \
\        Website:  http://pfind.org             /
  *********************************************

[pParse] C:\Users\Users\Documents\20250527_PRI_TIMS7_EVO2_DDA_60SPD_8cmPS_P410_R1660_X2867_FWG000014_S124_S2-E4_1_12404.d Converting to MS1 & MS2...
[pParse2Plus] 1, cfg_plus_args: {'path': {'pParse2': '..\pParse.exe', 'fpath_pcfg_mode': 2}, 'Plus': {'pXtract_n_isotope': 0}}
[pParse2Plus] 1, C:\Users\Users\Documents\20250527_PRI_TIMS7_EVO2_DDA_60SPD_8cmPS_P410_R1660_X2867_FWG000014_S125_S2-F4_1_12405.d
[cur] 2026-03-02 16:50:21 Starting...
[pParse2Plus] 1, Extract using pParse
[pParse2Plus] "C:\pFindStudio\pFind3\bin\pParse.exe" -D "C:\Users\Users\Documents\20250527_PRI_TIMS7_EVO2_DDA_60SPD_8cmPS_P410_R1660_X2867_FWG000014_S125_S2-F4_1_12405.d" -t -5 -z 5 -i 1 -C 1 -a 0 -p 1 -S 1 -b 0 -m 0 -P 1 -O "C:\Users\Users\Documents"

  *********************************************
 /       pParse2.0 (x64) from pFind Studio     \
/        Email  :  pfind@ict.ac.cn              \
\        Website:  http://pfind.org             /
  *********************************************

[pParse] C:\Users\Users\Documents\20250527_PRI_TIMS7_EVO2_DDA_60SPD_8cmPS_P410_R1660_X2867_FWG000014_S125_S2-F4_1_12405.d Converting to MS1 & MS2...
[pParse] == == == Time elapsed: 1 seconds. == == == =
[pParse] == == == Time elapsed: 1 seconds. == == == =
[pParse2Plus] 0, pParse2Plus has been extracted spectra before.
[pParse2Plus] 1, pParse2Plus has been extracted spectra before.
[pFind] ALERT: Invalid_msmspath1_Path: [C:\Users\Users\Documents\20250527_PRI_TIMS7_EVO2_DDA_60SPD_8cmPS_P410_R1660_X2867_FWG000014_S124_S2-E4_1_12404_CIDTOF.pf2]