Proteomics web tutorials from MSI

MSI has created web tutorials on using MaxQuant and Protein Pilot.


MaxQuant is a suite of algorithms for analysis of high-resolution mass spectrometry (Orbitrap) proteomics data.

  1. Introduction to MaxQuant (31 minutes)
  2. MaxQuant at MSI: Step by Step Guide by Rongxiao Sa (35 minutes)

Protein Pilot™

ProteinPilot™ is a proteomics software program used for analysis of peptide tandem mass spectrometry data and for relative quantification of proteins using the iTRAQ® technology and other modes of stable isotope labeling.

  1. Module One : Introduction to ProteinPilot by LeeAnn Higgins (23 minutes)
  2. Module Two : ProteinPilot Outputs (27 minutes)
  3. Module Three : ProteinPilot Peptide Summary by LeeAnn Higgins (21 minutes)
  4. Module Four : ProteinPilot Protein Summary and Quantitation (15 minutes)
  5. Module Five : False Discovery Rate Analysis and ProteinPilot FDR output (25 minutes)
  6. Module Six : Beyond ProteinPilot by LeeAnn Higgins (15 minutes)