Services and fees
We offer services for protein identification, characterisation, and quantification. We primarily follow a bottom-up approach, which involves digesting the proteins into peptides, identifying these peptides using LC-MS/MS and database searches, and reassembling them into proteins. Additionally, we offer intact protein mass determination under denaturing conditions using. Top-down approaches, applying fragmentation techniques to intact proteins are currently not offered as a standard service.
This includes protein digestion (from SDS-gel, in-solution, or beads), reduction and alkylation, a quality control run on an LC-UV-VIS system, high resolution accurate mass LC-MS/MS analysis, database search, qualitative data analysis, and the generation of an output file for the user. Depending on sample complexity we apply different gradient lengths.
Identification of post-translational modifications
We perform analysis of post-translational modifications with or without prior enrichment. We have extensive experience in the analysis of phosphorylation and lysine acetylation but we are open to integrate any other PTM of interest, if it is accessible by means of MS.
Our pipelines support quantitation of peptides and proteins, using metabolic (SILAC) or chemical (TMT, iTRAQ, dimethyl) labels as well as label-free approaches. Properly applied, these methods allow reliable quantification of a large number of proteins and their (modified) peptides in complex samples. However, careful experimental planning is key to the generation of useful data. In case you would like to perform such experiments we would be happy to assist in the planning phase.
Modern quantitative mass spectrometry can be an extremely valuable tool for identifying interacting proteins. Affinity-purification MS experiments (pull-downs, CoIPs, etc.) cannot only yield the identity of putatively interacting proteins but also their enrichment factor and the statistical significance of this enrichment - giving you more confidence for separating true interactors from background. We offer specialised workflows including quantitative and statistical data analysis for these type of experiments and we would be happy to discuss your experiments in detail.
Crosslinking mass spectrometry
Cross-linking mass spectrometry has evolved into a powerful technique which provides structural information and modelling constraints on proteins and protein complexes in solution (for a recent review see here). We offer a specialised workflow including digestion of cross-linked proteins in gel or in solution, LC-MS/MS measurement, and data analysis. MFPL users can follow this link for more detailed information on sample preparation. External users interested in our services please contact us.
Intact protein mass analysis
Determining the mass of an intact protein as accurately as possible is an extremely helpful tool. For example it may serve as quality control of expressed proteins, help to characterize possible chemical or post-translational modfications, examine truncation products, etc. We provide intact protein mass analysis under denaturing conditions using a high-resolution and accurate mass ESI-TOF-MS system, coupled to a micro-flow HPLC system for online desalting and separation. Native protein (complex) analysis and ion-mobility separation are not offered as a routine service but are available to a limited extent as research collaborations upon request.
Other protocols or sample preparation procedures
We provide a number of sample preparation techniques to maximize sample quality and depth of coverage, such as:
- In-gel, in-solution or filter-aided-digests
- Various sample clean-up strategies
- Sample fractionation for higher coverage in stage-tips or on HPLC
Please contact us for more details or if you are interested in other procedures not listed here.
MFPL users: Please follow this link for internal rates.
External users: Please contact us for a quote tailored to your specific needs. Please bear in mind that MFPL users have priority and external service can only be offered when there are free capacities.
We would like to point out that we will charge every run, irrespective of whether a desired result was obtained. As mentioned on our sample preparation page we cannot guarantee successful measurements for every sample, due to the intrinsic limitations of the sample preparation process and mass spectrometry. Unfortunately, such cases cannot be fully avoided but we try to minimize the risks. Certainly, in cases when technical or processing problems occur in the facility we will not charge for this sample or run.