Note: Scaffold DDA does support iTRAQ/TMT for all search engines in the broader product sense because these load paths can acquire peaklists/spectra. The MS3 iTRAQ/TMT column below is narrower: it is Yes only when that search-engine import path explicitly populates isobaric quant values.
| Search engine / import path | Label-Free | MS3 iTRAQ /TMT | SILAC | Notes |
| Mascot (direct DAT/MSR import) | No | No | No | Direct Mascot readers import identifications and spectra, but no explicit isobaric quant values are populated. |
| MSFragger | No | No | No | |
| FragPipe | Yes | No | No | Imports precursor intensity for label-free use, but no explicit isobaric quant values are populated. |
| Sage | Yes | No | No | Imports LFQ precursor intensities from Sage LFQ output when present, but no explicit isobaric quant values are populated. |
| MaxQuant / Andromeda | Yes | Yes | Yes | |
| Proteome Discoverer | Yes | Yes | Yes | |
| PD Nodes (via Proteome Discoverer MSF): Sequest, Sequest HT, Amanda, ZCore, Byonic, CHIMERYS | Yes | Yes | Yes | Proteome Discoverer quant tags are mapped separately from the search engine node. |
| Generic mzIdentML engines (for example Comet, OMSSA, PEAKS, X! Tandem, Byonic, Sequest) | Yes | No | No | The mzIdentML reader can load spectra/peaklists, but it does not create explicit isobaric or SILAC quant channels on its own. |