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