Support for timsTOF data

### Description of feature

I tested identification workflow for timsTOF dataset in last week. The first step is to execute the tdf2mzml module and then run the same analyses as for the other data (Comet and MSGF+). Then I compared results with MaxQuant. Set PSM FDR as 0.01, and results of MaxQuant are from evidence.txt. Then overlap of identified peptides above 90% from MaxQuant. But the overlap of PSM is 0. Because scan number (index) is different bwteen quantms and MQ after comparing precursor mz.

[compare_results.csv](https://github.com/user-attachments/files/17788538/compare_results.csv)
[compare_results_pep.zip](https://github.com/user-attachments/files/17788605/compare_results_pep.zip)

Some questions:
1. For example, the peptide is identified in three scans those are different MQ. How to compare and check the difference due to different scan numbers (or index)? I manually checked the identifications and they all look like they match well？

| sequence | exp_mass_to_charge | quantms scan_number | MaxQuant MS/MS scan number |
|---------------|--------------------|-----|----------------------|
| AAAAAAMAEQESAR | 695.3256725319 | 356222 | 65719 |
| AAAAAAMAEQESAR | 695.3256725319 | 356647 | 65719 |
| AAAAAAMAEQESAR | 695.3256725319 | 356088 | 65719 |


2. Surprised quantms identified so many peptides! I also manually checked the identifications in only quantms and they all look like they match not bad？ Further assessment is needed here