Scaffold, Q+/Q+S, PTM and perSPECtives Supported Data Formats


This document provides a comprehensive list of files compatible with the programs in the Scaffold Suite.


Due to how Byonic currently interfaces with Proteome Discoverer, Scaffold can only load data from Byonic run in PD versions 2.0 and 2.1. We have reached out to Byonic and are awaiting a resolution.

External Document Resources

Scaffold Suite File Compatibility Matrix: Common Search Engines



1. Byonic node supported in Proteome Discoverer 2.0 and 2.1

2. If the *.dat file is inaccessible from the server, it should be placed in the same directory as the *.xml and and *.rov files 

3. MaxQuant supported versions and higher

4. Run PD with appropriate templates for either precursor intensity, isobaric tags or stable isotope labeling

Scaffold Suite File Compatibility Matrix: Other Search Engines



1. Run PD with appropriate templates for precursor intensity, isobaric tags or stable isotope labeling

2. For IdentityE quantitation, the input files must be created from the Scaffold plugin installed in Waters PLGS version 2.4 or higher

3. Scaffold only supports modifications that are reported by Spectrum Mill as having single sites with a single formula

4. Decoy searches from unknown search engines that support mzIdentML exports

Scaffold PTM and Scaffold perSPECtives File Compatibility Matrix



1. In Scaffold PTM, labeled quantitation is included only when a ScaffoldQuantML (*.sqml) file exported from Scaffold Q+ or Q+S is loaded into Scaffold PTM

2. In Scaffold perSPECtives, precursor intensity is supported though mzIdentML exported from Scaffold. The Scaffold experiments need to include data process for precursor intensity quantitation through Spectrum Mill, Mascot Distiller, Proteome Discoverer, Protein Pilot or MaxQuant

3. Examples of incompatible tools include MS-GF+, MyriMatch, Peptidome and SpectraST, for more information see the Scaffold perSPECtives User Guide

Search Engine Versions Supported


Scaffold Export File Formats

Scaffold results are saved in the SF3 format, which can be opened in Scaffold or the Scaffold Viewer

Results may also be exported in the following formats:

  • mzIdentML - for PRIDE submission, Scaffold PTM, Scaffold perSPECtives, etc
  • protXML - ProteinProphet format
  • SFDB - opens directly in Scaffold perSPECtives
  • SQML - quantitative results from Scaffold Q+ experiments for Scaffold PTM

Reports generated by Scaffold are saved in CSV format, but the files names are given the file extension .xls to facilitate opening by Excel

Spectral Libraries may be exported in BLIB format for use in Skyline or Scaffold DIA

Spectra may be exported as:

  • Mascot MGF
  • Concatenated DTAs
  • Individual DTAs
  • Micromass PLKs

Images may be exported in a wide variety of formats, including:

  • WMF/EMF - Windows Metafile, to be pasted into Word or PowerPoint
  • SVG - Scalable Vector Graphics format produces an editable and scalable image for PowerPoint, Adobe Illustrator or other programs
  • PDF - Adobe Portable Document Format
  • PNG - Portable Network Graphics format
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