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Mass spectrometry services
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Mass spectrometry proteomics services

What is Proteomics?


Proteomics is the large scale study of all the proteins that can be found in a given sample. When using mass spectrometry to conduct your proteomics studies, you can gather information on the variation of the expression, post-translational modifications (PTMs) and even sub-cellular localization of the whole proteome between two experimental conditions. As with every other mass spec techniques, proteomics can be coupled with various preparation techniques in order to yield different types of information. Here are some examples of molecular biology techniques that we offer for your proteomics studies and the corresponding information that it can produce :


1. Classic sample preparation (click here for a video of the procedure)

This technique is used to digest proteins into peptides before the actual LC-MS/MS analysis. The proteins are first reduced and alkylated to prevent the formation of disulfide bonds (S-S) betweek cysteines before being digested by endoproteases, such as Trypsin, LysC and GluC. This preparation technique is ideal for a classic shotgun proteomics experiments and protein identification.


2. 2D LC-MS for proteomics

Two-dimension LC-MS (2D LC-MS) is a technique that relies on a double fractionation of the proteome to be analyzed. This technique is employed to either make the proteome less complex for the mass spectrometer to increase its sequencing depth (several injections of the fractionated sample) or to study sub-cellular localization. 2D LC-MS can be done with several fractionation techniques, such as organelle centrifugation, mass separation or hydrophobic interactions.


3. Affinity purification coupled to mass spectrometry (AP-MS)

Affinity purification (AP) is a method that uses the affinity of a molecule for different types of chemical groups to isolate the said molecule from its matrix. For example, by using magnetic beads coated with Titanium oxide groups, one can pull down the phospho-proteins from a whole proteome to analyse them by mass spectrometry. This process is pretty much the same as an immunoprecipitation, in that it enables the user to concentrate a group of molecule or proteins to facilitate their analysis. The use of AP in proteomics can greatly enhance the study of any PTMs that can be targeted by an antibody or a chemical group. It can also be used to analyze the interaction partners of a protein of interest.

Click here to contact our team of experts for your proteomics projects!

Our offer


PhenoSwitch Bioscience operates a state-of-the-art TripleTOF 5600 from SCIEX. This mass spectrometer offers the MS/MSall with SWATHTM acquisition mode, that enables the quantification of every ionisable molecule in the sample. With our SWATH proteomics services, you can have quantitative information for every detectable peptide of every protein in your sample, at the MS/MS level! The results can be used to monitor changes in protein expression between two samples, or to identify biomarkers. And as stated above, it is compatible with almost any sample preparation methods, such as 2D-LC/MS and AP-MS!


For more information on SWATH, please refer to our blog post on the matter. Also, you can see the kind of information we provide in a proteomics experiment by having a look at what our blog post on proteomics data report.


Of note, we also offer the good old shotgun proteomics approach for certain applications, such as post-translational modification and TAILS studies. Click on the button above to contact our experts and start a new proteomics project!

Proteomics services