| Links to protein tools | Mass Spec on Campus | Other Links |
| In Gel Digest Protocol | Mass Spec Class - Chem 638 | Madison Mass Spec Discussion Group |
| MALDI-MSI | Chemistry Mass Spec Facility | GLBRC |
| Matrix Science Mascot | School of Pharmacy | Madison Metabolomics Consortium |
| Protein Prospector | Biochemistry BIF | UW Comprehensive Cancer Center |
| NCBI OMSSA | Human Proteomics Program | Base Peak |
| The GPM | Medicago Group | ASMS |
| Delta Mass | Lingjun Li | VMSL |
| ExPASy | Lloyd Smith | ABRF |
| Trans-Proteomic Pipeline | Joshua Coon | XCMS |
| Scaffold Viewer | Michael Sussman | |