File formats
| bullseye | tide-index | tide-search | comet | percolator | spectral-counts | |
| MS1 | in | |||||
| MS2 (sample) / CMS2 | in/out | in | in | in | in | |
| MGF | in/out | in | in | in | ||
| mzML, mzXML | in | in | in | in | in | |
| Thermo .raw files (Windows only) | in | in | in | in | ||
| Other proprietary vendor formats (Windows only) | in | in | ||||
| FASTA (sample) | in | in | in | in | ||
| database index | out | in | ||||
| Tab-delimited text (sample) | out | out | in/out | in/out | ||
| pepXML | out | out | in/out | in | ||
| PIN | out | in | ||||
| POUT | out | |||||
| mzIdentML | out | out | out | in | ||
| SQT | out | out | in | in | ||
| Feature file | in/out | |||||
| Crux parameters (sample) | in/out | in/out | in/out | in/out | in/out | in/out |