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