Protein & Peptide Quantification

At the FGCZ, we quantify peptide mixtures mainly by mass spectrometry using either label free or isotope coded labels, which is 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
• SILAC - Stable Isotope Labelling of Amino acids in Culture (15N)
• AQUA - Absolute Quantitation using analogues

Label free:

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

Targeted quantitative proteomics approaches:

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

Details on our mass spectrometers.

Support Modes

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

Contacts

Doro Rutishauser - user lab