Differential Proteomics

Label-Free Technology

Label-Free technology includes various methods of relative quantification of proteins that do not require isotopic labeling. Unlike the methods of quantification based on isotopic labeling, the samples to be compared are analyzed separately. Label-Free methods thus provide a less accurate quantification than methods based on the isotopic labeling but they allow us to compare a larger number of samples and therefore constitute an interesting alternative.
Label-Free approaches are based either on the intensity of the detected peptides, or the number of MS/MS spectra acquired for each peptide (Spectral count). Protim uses these two approaches and relies on the quantification tools of the Proline software developed by ProFi (French Proteomics Infrastructure; www.profiproteomics.fr). We also use the method "Top 3" based on the measurement of intensity of the 3 most intense peptides available in the ProteomeDiscoverer software (Thermo Scientific), used for analysis of Orbitrap data.
  • Application example :

Determination of proteins differentially expressed in cells or tissues after treatment or induced by a disease state.

More or less complex sample comparison.


  • Application fields :

Cytosoluble and membrane proteins, Biological fluids


  • Publications with our lab :

Becker et al., 2017, J Proteomics.; 156: 5-19. doi: 10.1016/j.jprot.2016.12.016.

Colinet et al., 2017, Scientific Reports. 2017; 7(1): 1713. doi: 10.1038/s41598-017-01974-z.