Modules documentation

• Description of a module
• Downloading benchmarking data
• Parameters parsed for public submission
  • General comments on the parameters that are retrieved by ProteoBench
  • Tool-specific information

Links to active modules

• Label-free quantification of precursor ions with DDA (QExactive)

• Label-free quantification of peptidoforms with DDA (QExactive)

• Label-free quantification of precursor ions with DDA (Astral)

• Label-free quantification of precursor ions with DIA-PASEF

• Label-free quantification of precursor ions with DIA (Astral)

• Label-free quantification of precursor ions with DIA (ZenoTOF 8600 - ZenoSWATH)

• Label-free quantification of precursor ions with DIA (ZenoTOF 8600 - ZenoSWATH)

Links to the documentation of active modules

• Active Modules
  • DIA quantification - precursor ion level - SCIEX ZenoTOF 8600 system - Zeno SWATH DIA
  • De Novo - DDA - HCD (Alpha phase) [Work in Progress]
  • DDA quantification - precursor ion level (QExactive)
  • DDA quantification - peptidoform level (QExactive)
  • DIA quantification - precursor ion level - diaPASEF
  • DIA quantification - precursor ion level - Astral 2Th
  • DDA quantification - precursor ion level - Astral
  • DIA quantification - precursor ion level - Single Cell

Links to archived modules

• Label-free quantification of precursor ions with DIA (AIF): A discussion on oxidation-related issues with the data used for this module can be found here, and the documentation here.

Links to documentation of archived modules

• Archived Modules
  • DIA quantification - precursor ions - AIF data