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Installation Instructions for timsread

timsread is a C++ tool for reading Bruker TimsTOF (TDF) files

g++ -O3 -march=native -std=c++17 -I../timsdata_5_0_2/timsdata/include/c   -I../timsdata_5_0_2/timsdata/examples/timsdataSampleCpp/timsdataSampleCpp   -o timsread timsread.cpp   -L../timsdata_5_0_2/timsdata/linux64 -ltimsdata -lsqlite3
LD_LIBRARY_PATH=../timsdata_5_0_2/timsdata/linux64 ./timsread 230317_SIGRID_10_Slot1-41_1_4086.d

Table of Contents

  1. Download Required SDK and Libraries
  2. Extract Files
  3. Install System Dependencies
  4. Set Up Include Paths
  5. Compile
  6. Run

TBD

  1. Nextflow Pipeline
  2. Performance Notes
  3. Quality Comparison

1. Download Required SDK and Libraries

2. Extract Files

  • Extract timsdata_5_0_2.zip to a directory, e.g., ../timsdata_5_0_2.

3. Install System Dependencies (on Debian/Ubuntu/WSL2)

sudo apt-get update
sudo apt-get install -y g++ sqlite3 libsqlite3-dev

4. Set Up Include Paths

You will need the following include directories:

  • ../timsdata_5_0_2/timsdata/include/c (contains timsdata.h)
  • ../timsdata_5_0_2/timsdata/examples/timsdataSampleCpp/timsdataSampleCpp (contains timsdata_cpp.h)

5. Compile

From the project directory, run:

g++ -O3 -march=native -std=c++17 -I../timsdata_5_0_2/timsdata/include/c   -I../timsdata_5_0_2/timsdata/examples/timsdataSampleCpp/timsdataSampleCpp   -o timsread timsread.cpp   -L../timsdata_5_0_2/timsdata/linux64 -ltimsdata -lsqlite3
  • Adjust the ../timsdata_5_0_2/timsdata/ paths if your files are located elsewhere.
  • On Windows, use the appropriate path format and a compatible compiler (e.g., MSVC).

6. Run

The program converts Bruker TDF files to MGF format for MS/MS spectra and optionally extracts MS1 data.

Usage:

Data Sources:

  • PXD045439: 230317_SIGRID_10_Slot1-41_1_4086.d
# Download example dataset
wget https://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD045439/230317_SIGRID_10_Slot1-41_1_4086.d.tar
tar xvf 230317_SIGRID_10_Slot1-41_1_4086.d.tar
# sanity check
sudo apt install sqlite3
sqlite3 "230317_SIGRID_10_Slot1-41_1_4086.d/analysis.tdf" "SELECT COUNT(*) as null_mz FROM Precursors WHERE MonoisotopicMz IS NULL; SELECT COUNT(*) as negative_mz FROM Precursors WHERE MonoisotopicMz < 0;"
5314
0

set library path and run:

# Extract chromatogram data 
LD_LIBRARY_PATH=../timsdata_5_0_2/timsdata/linux64 ./timsread -chrom 230317_SIGRID_10_Slot1-41_1_4086.d 
# Extract SQL data only (faster)
LD_LIBRARY_PATH=../timsdata_5_0_2/timsdata/linux64 ./timsread -sql 230317_SIGRID_10_Slot1-41_1_4086.d
# Extract SQL data only (default)
LD_LIBRARY_PATH=../timsdata_5_0_2/timsdata/linux64 ./timsread -mgf 230317_SIGRID_10_Slot1-41_1_4086.d
# Extract both MS/MS and MS1 data sampled at 10th frame (little faster)
LD_LIBRARY_PATH=/mnt/z/Download/timsdata-2.21.0.4/timsdata/linux64 ./timsread "230317_SIGRID_10_Slot1-41_1_4086.d" -ms1
# Extract ALL of TDF data
LD_LIBRARY_PATH=../timsdata_5_0_2/timsdata/linux64 ./timsread -tdf 260506_peptid_p10_Slot2-1_1_13559.d
# Extract ALL of TDF_bin data
LD_LIBRARY_PATH=../timsdata_5_0_2/timsdata/linux64 ./timsread -tdfbin 260506_peptid_p10_Slot2-1_1_13559.d

Takes few minutes and expected default MGF output:

time LD_LIBRARY_PATH=../timsdata_5_0_2/timsdata/linux64 ./timsread 230317_SIGRID_10_Slot1-41_1_4086.d
# Calibration     : instrument default
Loading metadata...
# TDF file          : 230317_SIGRID_10_Slot1-41_1_4086.d
# Total frames      : 66477
# Precursors loaded : 291844
# MS/MS frames      : 56501
# MGF output        : 230317_SIGRID_10_Slot1-41_1_4086.d_msms.mgf
Processing frames...
Progress: 100% (66477/66477) MS1:0 MS2:56501 
Total frames processed : 66477
MS1 frames             : 0
MS/MS frames           : 56501
Skipped (invalid m/z)  : 8268
MGF extraction completed.

real    6m47.663s
user    3m54.451s
sys     0m16.221s

Expected output with -ms1 switch:

time LD_LIBRARY_PATH=../timsdata_5_0_2/timsdata/linux64 ./timsread2 -ms1 230317_SIGRID_10_Slot1-41_1_4086.d
# Calibration     : instrument default
Loading metadata...
# TDF file          : 230317_SIGRID_10_Slot1-41_1_4086.d
# Total frames      : 66477
# Precursors loaded : 291844
# MS/MS frames      : 56501
# MGF output        : 230317_SIGRID_10_Slot1-41_1_4086.d_msms.mgf
# MS1 output        : 230317_SIGRID_10_Slot1-41_1_4086.d_ms1.txt
Processing frames...
Progress: 100% (66477/66477) MS1:9975 MS2:56501 
Total frames processed : 66477
MS1 frames             : 9976
MS/MS frames           : 56501
Skipped (invalid m/z)  : 8268
MGF extraction completed.

real    16m24.490s
user    11m0.906s
sys     0m38.002s

Output Files:

  • *.d_msms.mgf: MS/MS spectra in MGF format for protein identification
  • *.d_ms1.txt: MS1 spectra (if -ms1 flag used) with format: Frame_ID RT_seconds Scan_Number m/z Intensity Mobility

Expected output with -tdf switch:

time LD_LIBRARY_PATH=../timsdata_5_0_2/timsdata/linux64 ./timsread2 -tdf 230317_SIGRID_10_Slot1-41_1_4086.d
Dumping all TDF tables from 230317_SIGRID_10_Slot1-41_1_4086.d ...

--- analysis.tdf tables (230317_SIGRID_10_Slot1-41_1_4086.d/analysis.tdf) ---
  Found view: Properties
  Found table: CalibrationInfo
  Found table: CollisionEnergySweepingInfo
  Found table: DiaFrameMsMsInfo
  Found table: DiaFrameMsMsWindowGroups
  Found table: DiaFrameMsMsWindows
  Found table: ErrorLog
  Found table: FrameMsMsInfo
  Found table: FrameProperties
  Found table: Frames
  Found table: GlobalMetadata
  Found table: GroupProperties
  Found table: MzCalibration
  Found table: PasefFrameMsMsInfo
  Found table: Precursors
  Found table: PrmFrameMeasurementMode
  Found table: PrmFrameMsMsInfo
  Found table: PrmTargets
  Found table: PropertyDefinitions
  Found table: PropertyGroups
  Found table: Segments
  Found table: TimsCalibration

Dumping 22 tables/views...
  Properties                        28651587 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_Properties.txt
  CalibrationInfo                         27 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_CalibrationInfo.txt
  CollisionEnergySweepingInfo              0 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_CollisionEnergySweepingInfo.txt
  DiaFrameMsMsInfo                         0 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_DiaFrameMsMsInfo.txt
  DiaFrameMsMsWindowGroups                 0 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_DiaFrameMsMsWindowGroups.txt
  DiaFrameMsMsWindows                      0 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_DiaFrameMsMsWindows.txt
  ErrorLog                                 0 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_ErrorLog.txt
  FrameMsMsInfo                            0 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_FrameMsMsInfo.txt
  FrameProperties                    9145262 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_FrameProperties.txt
  Frames                               66477 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_Frames.txt
  GlobalMetadata                          36 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_GlobalMetadata.txt
  GroupProperties                        267 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_GroupProperties.txt
  MzCalibration                            1 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_MzCalibration.txt
  PasefFrameMsMsInfo                  542469 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_PasefFrameMsMsInfo.txt
  Precursors                          291844 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_Precursors.txt
  PrmFrameMeasurementMode                  0 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_PrmFrameMeasurementMode.txt
  PrmFrameMsMsInfo                         0 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_PrmFrameMsMsInfo.txt
  PrmTargets                               0 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_PrmTargets.txt
  PropertyDefinitions                    431 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_PropertyDefinitions.txt
  PropertyGroups                           1 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_PropertyGroups.txt
  Segments                                 1 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_Segments.txt
  TimsCalibration                          1 rows -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_TimsCalibration.txt

--- analysis.tdf_bin SDK calibration ---
  Frame 1 (MS1)  mz_calib -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_calib_mz_frame1_MS1.txt
             1k0_calib -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_calib_1k0_frame1_MS1.txt
  Frame 8 (MS1)  mz_calib -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_calib_mz_frame8_MS1.txt
             1k0_calib -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_calib_1k0_frame8_MS1.txt
  Frame 19 (MS1)  mz_calib -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_calib_mz_frame19_MS1.txt
             1k0_calib -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_calib_1k0_frame19_MS1.txt
  Frame 2 (MS2)  mz_calib -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_calib_mz_frame2_MS2.txt
             1k0_calib -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_calib_1k0_frame2_MS2.txt
  Frame 3 (MS2)  mz_calib -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_calib_mz_frame3_MS2.txt
             1k0_calib -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_calib_1k0_frame3_MS2.txt
  Frame 4 (MS2)  mz_calib -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_calib_mz_frame4_MS2.txt
             1k0_calib -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_calib_1k0_frame4_MS2.txt
  Calibration summary -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdf/230317_SIGRID_10_Slot1-41_1_4086.d_calib_summary.txt

Output directory: 230317_SIGRID_10_Slot1-41_1_4086.d_tdf

real    3m54.514s
user    1m4.579s
sys     0m10.615s

-tdfbin switch: note that timsread warns about the sizes, default is to NOT proceed, press y to continue...

time LD_LIBRARY_PATH=../timsdata_5_0_2/timsdata/linux64 ./timsread2 -tdfbin 230317_SIGRID_10_Slot1-41_1_4086.d

=== analysis.tdf_bin full extraction ===
  MS1 : 9976 frames, 2183426604 peaks  ->  ~131.0 GB  (250 chunk(s))
  MS2 : 56501 frames, 302769315 peaks  ->  ~18.2 GB  (35 chunk(s))
  Total                     ->  ~149.2 GB

  Output: 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/
  Format: Frame_ID  RT_seconds  MsMsType  Scan  mz  Intensity  1_over_K0

Proceed? This will write ~149.2 GB to disk. [y/N] y
# Calibration: instrument default
Extracting...
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk001.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk001.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk002.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk003.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk004.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk005.txt
  3% (2000/66477)  written: 37993500 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk006.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk007.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk008.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk009.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk010.txt
  6% (4000/66477)  written: 87909012 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk011.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk012.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk013.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk014.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk015.txt
  9% (6000/66477)  written: 137840553 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk002.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk016.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk017.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk018.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk019.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk020.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk021.txt
  12% (8000/66477)  written: 195101362 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk003.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk022.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk023.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk024.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk025.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk026.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk027.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk004.txt
  15% (10000/66477)  written: 260785761 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk028.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk029.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk030.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk031.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk032.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk005.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk033.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk034.txt
  18% (12000/66477)  written: 334044735 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk035.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk036.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk037.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk006.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk038.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk039.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk040.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk041.txt
  21% (14000/66477)  written: 413693242 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk042.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk043.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk007.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk044.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk045.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk046.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk047.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk048.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk008.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk049.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk050.txt
  24% (16000/66477)  written: 500062311 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk051.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk052.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk053.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk009.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk054.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk055.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk056.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk057.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk058.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk059.txt
  27% (18000/66477)  written: 595191853 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk010.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk060.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk061.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk062.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk063.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk064.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk011.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk065.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk066.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk067.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk068.txt
  30% (20000/66477)  written: 693250874 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk069.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk012.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk070.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk071.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk072.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk073.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk074.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk075.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk013.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk076.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk077.txt
  33% (22000/66477)  written: 790609480 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk078.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk079.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk080.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk014.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk081.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk082.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk083.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk084.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk085.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk086.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk015.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk087.txt
  36% (24000/66477)  written: 893505174 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk088.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk089.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk090.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk091.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk016.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk092.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk093.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk094.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk095.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk096.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk017.txt
  39% (26000/66477)  written: 996375270 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk097.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk098.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk099.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk100.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk101.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk018.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk102.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk103.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk104.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk105.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk106.txt
  42% (28000/66477)  written: 1102324455 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk107.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk019.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk108.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk109.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk110.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk111.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk112.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk020.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk113.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk114.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk115.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk116.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk117.txt
  45% (30000/66477)  written: 1212696272 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk021.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk118.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk119.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk120.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk121.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk122.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk123.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk022.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk124.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk125.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk126.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk127.txt
  48% (32000/66477)  written: 1322887796 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk128.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk023.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk129.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk130.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk131.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk132.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk133.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk134.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk024.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk135.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk136.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk137.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk138.txt
  51% (34000/66477)  written: 1435017981 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk139.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk140.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk025.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk141.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk142.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk143.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk144.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk145.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk026.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk146.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk147.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk148.txt
  54% (36000/66477)  written: 1540412319 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk149.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk150.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk151.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk027.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk152.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk153.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk154.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk155.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk156.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk157.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk028.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk158.txt
  57% (38000/66477)  written: 1644256584 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk159.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk160.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk161.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk162.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk163.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk029.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk164.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk165.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk166.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk167.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk168.txt
  60% (40000/66477)  written: 1754867096 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk169.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk030.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk170.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk171.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk172.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk173.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk174.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk175.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk176.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk031.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk177.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk178.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk179.txt
  63% (42000/66477)  written: 1863583404 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk180.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk181.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk182.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk183.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk032.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk184.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk185.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk186.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk187.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk188.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk189.txt
  66% (44000/66477)  written: 1966560084 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk190.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk191.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk192.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk193.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk194.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk033.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk195.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk196.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk197.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk198.txt
  69% (46000/66477)  written: 2056741779 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk199.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk200.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk201.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk202.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk203.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk204.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk205.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk206.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk034.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk207.txt
  72% (48000/66477)  written: 2137333048 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk208.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk209.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk210.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk211.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk212.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk213.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk214.txt
  75% (50000/66477)  written: 2205757158 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk215.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk216.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk217.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk218.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk219.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk220.txt
  78% (52000/66477)  written: 2262182638 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk221.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk222.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk223.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk224.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk225.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms2_chunk035.txt
  81% (54000/66477)  written: 2308207166 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk226.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk227.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk228.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk229.txt
  84% (56000/66477)  written: 2345439571 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk230.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk231.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk232.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk233.txt
  87% (58000/66477)  written: 2380134380 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk234.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk235.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk236.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk237.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk238.txt
  90% (60000/66477)  written: 2423251002 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk239.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk240.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk241.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk242.txt
  93% (62000/66477)  written: 2463280687 peaks     -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk243.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk244.txt
  -> 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/230317_SIGRID_10_Slot1-41_1_4086.d_ms1_chunk245.txt
  100% (66477/66477)  written: 2486195849 peaks   

Done.
  Total peaks written : 2486195919
  MS1 chunks          : 245
  MS2 chunks          : 35
  Output              : 230317_SIGRID_10_Slot1-41_1_4086.d_tdfbin/

real    90m7.122s
user    69m55.285s
sys     1m3.252s

TBD

7. Nextflow Pipeline

This repository includes a Nextflow pipeline (nextflow.nf) for automated processing of TDF files using the timsread tool.

Prerequisites for Nextflow Pipeline:

  • Nextflow installed
  • Bruker timsdata SDK available at timsdata/linux64
  • Compiled timsread executable in the project directory

Pipeline Usage:

# Extract MS/MS spectra only (default, faster)
nextflow run nextflow.nf --input 230317_SIGRID_10_Slot1-41_1_4086.d

# Extract both MS/MS and MS1 spectra
nextflow run nextflow.nf --input 230317_SIGRID_10_Slot1-41_1_4086.d --ms2_only False

# Custom output directory
nextflow run nextflow.nf --input <tdf_directory> --publishdir custom_output

Pipeline Features:

  • Automated Processing: Handles library path configuration and tool execution
  • Scalable: Can process multiple TDF files in parallel
  • Flexible Output: Optional MS1 extraction with --ms2_only False
  • Quality Control: Generates summary statistics for processed files
  • Resume Capability: Use -resume to continue interrupted runs

Pipeline Output:

  • MGF Files: MS/MS spectra ready for protein identification
  • MS1 Files: Optional MS1 spectra data (if requested)
  • Summary Report: results_file.tsv with processing statistics

Example Pipeline Run:

# Download and extract test dataset
wget https://ftp.pride.ebi.ac.uk/pride/data/archive/2024/06/PXD045439/230317_SIGRID_10_Slot1-41_1_4086.d.tar
tar xf 230317_SIGRID_10_Slot1-41_1_4086.d.tar

# Run Nextflow pipeline
nextflow run nextflow.nf --input 230317_SIGRID_10_Slot1-41_1_4086.d

# Check results
ls nf_output/
# Output: 230317_SIGRID_10_Slot1-41_1_4086.d_msms.mgf  results_file.tsv

Notes

  • Ensure all required header and source files are present in the specified directories.
  • If you encounter missing dependencies, verify the include paths and that all SDK/library files are extracted.
  • The program automatically skips precursors with invalid (NULL) m/z values from the database.
  • Use -ms1 flag only when needed as MS1 extraction significantly increases processing time and output file size.
  • For automated processing: Use the included Nextflow pipeline (see Section 7) which handles library paths and batch processing automatically.

If you see an error about libtimsdata.so not being found, you must set the LD_LIBRARY_PATH environment variable to the directory containing libtimsdata.so as shown above. This only affects the current terminal session.

Performance Notes

Technical Details:

  • Zero-filter approach: Removes only zero-intensity peaks for maximum data retention
  • Optimized extraction: ~83% more spectra than Bruker's default export
  • Batch processing: Efficient handling of large datasets (66K+ frames)
  • Memory management: 4MB I/O buffers with periodic flushing

Quality Comparison

Our timsread extraction finds ~83% more spectra than Bruker's default MGF export due to:

  • More comprehensive PASEF precursor extraction
  • Less aggressive intensity filtering (zero-filter only)
  • Complete processing of all MS/MS frames and precursors

Example comparison:

  • Bruker export: 291,843 spectra
  • timsread extraction: 534,186 spectra (+83% more data)

why?

grep -A 30 "PEPMASS=1221.98873 17379" "230317_SIGRID_10_Slot1-41_1_4086.d/230317_SIGRID_10_Slot1-41_1_4086_6.0.313.mgf"
grep -A 50 "PEPMASS=1221.988770" "230317_SIGRID_10_Slot1-41_1_4086.d_msms.mgf"

Key Differences in Ion Handling? Bruker's Export (1 spectrum):

PEPMASS=1221.98873 17379
  • 15 peaks total
  • Peak at 1221.98649: 11508 intensity
  • Peak at 1222.99170: 4364 intensity
  • Clean, merged spectrum

Our timsread (Multiple spectra for same m/z):

PEPMASS=1221.988770 28038  (First occurrence)
PEPMASS=1221.988770 10418  (Second occurrence) 
PEPMASS=1221.988770 10418  (Third occurrence)
PEPMASS=1221.988770 21162  (Fourth occurrence)
PEPMASS=1221.988770 3872   (Fifth occurrence)
PEPMASS=1221.988770 3872   (Sixth occurrence)
PEPMASS=1221.988770 10789  (Seventh occurrence)
PEPMASS=1221.988770 10789  (Eighth occurrence)
PEPMASS=1221.988770 18410  (Ninth occurrence)

Critical Discovery:

Bruker merges multiple PASEF precursors with the same m/z into a single spectrum, while our method creates separate spectra for each PASEF precursor instance. This probably explains:

  • Why we have 83% more spectra - We're not merging duplicate m/z precursors
  • Different intensity values - Each instance has its own intensity
  • Duplicate peaks - Same m/z fragments appear multiple times across different scans
Bruker's Approach:
  • Groups precursors by m/z
  • Merges peaks from multiple PASEF instances
  • Results in fewer, but "cleaner" spectra
Our Approach:
  • Each PASEF precursor gets its own spectrum
  • Preserves scan-level detail and timing information
  • More comprehensive but with redundancy

License

This repository is a fork of gtluu/timsconvert, originally licensed under the Apache License 2.0.

All original code is © the original authors and remains under Apache 2.0.

Modifications and additional contributions by Animesh Sharma
are © 2023–2025 and are available under the same Apache 2.0 license.
To the extent possible, Animesh Sharma’s contributions may also be reused under the MIT License.
See NOTICE and LICENSE-ANIMESH.md for details.

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