Whether .RAW files can be searched in Philosopher

[Bin-cc]

Hi,

I have noticed that .mzml files are recommended to search for AP-MS data in this, but I still want to ask if it is possible to use .raw files to search. I have tried to change spectra format as raw in philosopher.yml (search engine is msfragger), and it can work. However, It cannot successfully export the protein.tsv file since the .mzml file can not be found. Is it really impossible to search using raw files, or there are other methods？

Thank you. And part of run log is as follow.

Finished.
INFO[15:29:20] Executing filter on C:\Users\18811\Desktop\PRPF31_raw\PRPF31_1
INFO[15:29:20] Processing peptide identification files
INFO[15:29:21] 1+ Charge profile                             decoy=0 target=0
INFO[15:29:21] 2+ Charge profile                             decoy=50 target=3314
INFO[15:29:21] 3+ Charge profile                             decoy=43 target=1798
INFO[15:29:21] 4+ Charge profile                             decoy=11 target=287
INFO[15:29:21] 5+ Charge profile                             decoy=0 target=20
INFO[15:29:21] 6+ Charge profile                             decoy=0 target=0
INFO[15:29:21] Database search results                       ions=5148 peptides=4517 psms=5523
INFO[15:29:21] Converged to 1.00 % FDR with 5267 PSMs        decoy=53 threshold=0.2433 total=5320
INFO[15:29:21] Converged to 1.00 % FDR with 4265 Peptides    decoy=43 threshold=0.357 total=4308
INFO[15:29:21] Converged to 0.99 % FDR with 4910 Ions        decoy=49 threshold=0.2575 total=4959
INFO[15:29:23] Protein inference results                     decoy=51 target=3256
INFO[15:29:23] Converged to 1.07 % FDR with 1031 Proteins    decoy=11 threshold=0.9826 total=1042
INFO[15:29:23] 2D FDR estimation: Protein mirror image       decoy=1031 target=1031
INFO[15:29:23] Second filtering results                      ions=4786 peptides=4157 psms=5158
INFO[15:29:23] Converged to 0.05 % FDR with 5155 PSMs        decoy=3 threshold=0.0502 total=5158
INFO[15:29:23] Converged to 0.07 % FDR with 4154 Peptides    decoy=3 threshold=0.0595 total=4157
INFO[15:29:23] Converged to 0.06 % FDR with 4783 Ions        decoy=3 threshold=0.0502 total=4786
INFO[15:29:24] Post processing identifications
INFO[15:29:26] Mapping modifications
INFO[15:29:27] Processing protein inference
INFO[15:29:39] Assigning protein identifications to layers
INFO[15:29:40] Updating razor PSM assignment to proteins
INFO[15:29:40] Calculating spectral counts
INFO[15:29:40] Saving
INFO[15:29:40] Executing filter on C:\Users\18811\Desktop\PRPF31_raw\PRPF31_2
INFO[15:29:40] Processing peptide identification files
INFO[15:29:41] 1+ Charge profile                             decoy=0 target=0
INFO[15:29:41] 2+ Charge profile                             decoy=36 target=2506
INFO[15:29:41] 3+ Charge profile                             decoy=18 target=990
INFO[15:29:41] 4+ Charge profile                             decoy=2 target=108
INFO[15:29:41] 5+ Charge profile                             decoy=0 target=0
INFO[15:29:41] 6+ Charge profile                             decoy=0 target=0
INFO[15:29:41] Database search results                       ions=3452 peptides=3081 psms=3660
INFO[15:29:41] Converged to 0.99 % FDR with 3532 PSMs        decoy=35 threshold=0.3191 total=3567
INFO[15:29:41] Converged to 0.97 % FDR with 2967 Peptides    decoy=29 threshold=0.4105 total=2996
INFO[15:29:41] Converged to 0.98 % FDR with 3343 Ions        decoy=33 threshold=0.347 total=3376
INFO[15:29:43] Protein inference results                     decoy=51 target=3256
INFO[15:29:43] Converged to 1.07 % FDR with 1031 Proteins    decoy=11 threshold=0.9826 total=1042
INFO[15:29:43] 2D FDR estimation: Protein mirror image       decoy=1031 target=1031
INFO[15:29:43] Second filtering results                      ions=3296 peptides=2927 psms=3502
INFO[15:29:43] Converged to 0.05 % FDR with 3500 PSMs        decoy=2 threshold=0.0506 total=3502
INFO[15:29:43] Converged to 0.06 % FDR with 2925 Peptides    decoy=2 threshold=0.0832 total=2927
INFO[15:29:43] Converged to 0.06 % FDR with 3294 Ions        decoy=2 threshold=0.0617 total=3296
INFO[15:29:44] Post processing identifications
INFO[15:29:46] Mapping modifications
INFO[15:29:47] Processing protein inference
INFO[15:29:59] Assigning protein identifications to layers
INFO[15:30:00] Updating razor PSM assignment to proteins
INFO[15:30:00] Calculating spectral counts
INFO[15:30:00] Saving
INFO[15:30:00] Executing label-free quantification on C:\Users\18811\Desktop\PRPF31_raw\PRPF31_1
INFO[15:30:01] Indexing PSM information
INFO[15:30:01] Reading spectra and tracing peaks
INFO[15:30:01] Processing b9228_PRPF31
FATA[15:30:01] Cannot read file. open C:\Users\18811\Desktop\PRPF31_raw\PRPF31_1\b9228_PRPF31.mzML: The system cannot find the file specified.

[prvst]

Hi @Bin-cc. The upcoming version of Philosopher will have full (Thermo) raw support. Please keep an eye on the releases.

[Bin-cc]

Hi,

That's really good news, I will continue to pay attention.