## 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