How are protein abundances calculated?

Detection and quantification of all peptide ions is followed by expression analysis and identification of the proteins from which they originate.

Quantitation methods

Progenesis QI for proteomics provides a number of protein quantitation methods to choose from.

Please see the sections below for an explanation of each of these methods:

1. Absolute quantitation using Hi-N
2. Relative quantitation using Hi-N
3. Relative quantitation using non-conflicting peptides
4. Relative quantitation using all peptides

Features of protein quantitation

1. Co-detection of features provides ion abundance measures for the same peptides from each protein on every run, with no missing values
2. Summing means that ion abundances with higher signal, and therefore less “noisy”, have more weight; making the final protein quantification more reliable
3. Searching peptides against databases can return multiple entries that are actually the same or related proteins, so the software automatically groups similar proteins into one quantification result
4. Fractionated proteins are quantified in the same way but include all peptides from every fraction

See also

• Which quantitation method should I choose for my experiment?
• How are peptide ion abundances calculated?