Proteomics services

All proteomics services are performed on the Thermo Scientific Orbitrap Fusion tribrid mass spectrometer equipped with a Dionex UltiMate 3000 reverse-phase nano-UHPLC system.

Protein identification

We offer:

  • Identification of proteins from gel bands
  • Protein and peptide identification in solution, including identity confirmation of single, purified proteins, as well as large-scale protein identification in complex samples

Sample requirements

For gel samples, excise the band of interest and cut it into approximately 1-2 mm2 pieces. Place these in an Eppendorf tube and submit. Please provide an approximation of protein amount and information on the stain used in the submission form.

For in-solution samples, we require a minimum of 10 ug of protein for analysis. PEG, glycerol and detergents are not compatible with mass spectrometric analysis and must be removed prior to sample submission. Please provide details on the buffer composition in the submission form.

Quantitative proteomics

As standard, we offer label-free quantitation (LFQ) as no specific sample pre-treatment is required. For LFQ, each sample is analyzed separately by LC-MS/MS and the results are subsequently compared across all samples to yield relative quantitation data.

Labelling of proteins for quantitation can be employed to enable multiplexed measurements (that is, samples are pooled together analyzed in a single LC-MS/MS experiment). There are several options for consideration:

  • SILAC (Stable isotope labelling by amino acids in cell culture) is suitable for comparing the abundance of proteins in cell culture under two different conditions. Labelling is performed at the cell culture stage during protein expression.
  • TMT (Tandem mass tags), iTRAQ and similar labelling systems can be used to label proteins and peptides following their extraction. A larger number of conditions (up to 11 for TMT) can be simultaneously compared.

Targeted quantitation of specific proteins for increased accuracy can be carried out by parallel reaction monitoring (PRM). PRM requires dedicated method development for each target and will thus be more time-consuming than other approaches.

Sample requirements

Requirements are similar to those for protein identification; we need a minimum of 10 ug of protein for analysis. We recommend submitting three biological replicates for quantitation.

Post-translational modification analysis

We offer the identification and localization of acetylation, methylation, phosphorylation, glycosylation and other modifications by LC-MS/MS. Analysis of post-translational modifications can be performed as part of qualitative or quantitative experiments. In certain cases, enrichment of modified peptides may be necessary prior to sample submission.

Other analyses

Other, non-routine experiments may be developed and offered on an individual basis. If you wish to start a new project, please contact Klaudia Kocurek to schedule a consultation prior to submitting samples.