Quantitative proteomics

Label-free differential proteomics: Relative quantification

The principle of this strategy is to compare in a quantitative fashion, tryptic peptides digest of complex samples and spiked with different commercial internal standards which allows their relative quantification. The high sensitivity, resolution and mass accuracy of the mass spectrometer allow confident identification of the peptides and proteins present in the samples to be compared.

 

The generated LC-MS/MS data are submitted to database search using open-source software MaxQuant. After this step of identification and normalization, the data can be compared and submitted to statistical analysis using open-source software Perseus.

More information on these softwares.

 

Please note that for the study to be statistically relevant, each condition to be compared should be represented by at least biological triplicates.

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Absolute quantification of a known and targeted protein by Liquid Chromatography coupled to isotope dilution mass spectrometry

An identified protein of interest can be quantified in a complex mixture by the method developed in "Kirsch et al. Journal of Chromatography A (2007), 1153 (1-2), 300-306".

Each protein case is unique and must be subjected to a feasibility study before any further routine measurements.

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