Protein & Peptide Quantification

At the FGCZ, we quantify peptide mixtures mainly by mass spectrometry using either label free or isotope coded labels, as described here.

Alternatively individual and purified proteins are quantified by Amino Acid Analysis (see Support Modes > Protein Service > Amino Acid Analysis).

Mass Spectrometry-Based Quantification

Labeling technologies:

• iTRAQ - labels amino groups. Quantification via reporter ions in MS2
  --> iTRAQ publication
• SILAC - Stable Isotope Labelling of Amino acids in Culture (15N)
  --> SILAC publication
• AQUA - Absolute Quantitation using analogues
  --> AQUA publication

Label free:

• emPAI - Exponentially Modified Protein Abundance Index
  --> emPAI publication
• Progenesis LC-MS (commercial software solution from nonlinear dynamics)
  --> Label-free publication
• T3PQ - Top 3 protein quantification (in-house implementation of the Hi3 idea of waters)
  --> Label-free publication
• Spectral counting - Methods based on spectrum counting such as APEX or Scaffold are supported
  --> APEX publication
  --> Scaffold software

Targeted quantitative proteomics approaches:

• multiplexed Selected reaction monitoring analysis (mSRM also known as MRM) are supported with our triple quadrupole instruments
  --> MRM publication

Details on our mass spectrometers.

Support Modes

Protein & peptide Quantification is available as Protein Service and as User Lab project.

Contacts

Bernd Roschitzki - User Lab

Asa Wahlander - User Lab