The following table lists the file extensions for saved experiment files and their associated programs as well as input files. Files are program specific and therefore can only be opened by the program that was used to create it.
| Program | Input Files | File Extension |
| Scaffold, Scaffold Q+S | MZID, Search Engine result files | SF3 |
| Scaffold PTM | MZID (from Scaffold, Mascot or PEAKS) | SPTM |
| Scaffold LFQ / Scaffold perSPECtives | MZID (from Scaffold or Search Engine)* | SFDB |
| Scaffold DIA | Instrument RAW files | SDIA |
| Scaffold Elements | Instrument RAW files | METDB |
Click on the links above to access the individual program supported data formats documentation for a more detailed list of what files can be loaded into each program.
* Note, mzIdentML files from some search engines are not compatible with Scaffold LFQ. See the Scaffold LFQ User Guide for a list of search engines not directly compatible with LFQ.