Table 7. DDA Data Analysis Software Examples.
| Name | Publication | Website | Free/Paid |
|---|---|---|---|
| MaxQuant | Cox and Mann, 2008628 | MaxQuant | |
| MSFragger | Kong et al., 2017629 | MSFragger | free |
| Mascot | Perkins et al., 1999630 | Mascot | free |
| MS-GF+ | Kim et al.631 | MS-GF+ | free |
| X!Tandem | Craig et al.632,633 | GPMDB | free |
| Comet | Eng et al., 2012634 | Comet | free |
| Skyline | MacLean et al., 2010635 | Skyline | free |
| ProteomeDiscoverer | ProteomeDiscoverer | paid | |
| Mascot | Perkins et al., 1999630 | Mascot | paid |
| Spectromine | Spectromine | paid | |
| PEAKS | Tran et al., 2018636 | PEAKS | paid |