Services and fees

We offer an array of standard services for protein identification and characterisation. 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 determinaton under denaturing conditions using. Top-down approaches, applying fragmentation techniqes to intact proteins are currently not offered as a standard service.

Protein identification

Identification of post-translational modifications

Quantitative analyses

Interaction proteomics

Cross-linking MS

Intact protein mass analysis

Other protocols


Fees

How and when to acknowledge a contribution of the facility

 

Protein identification

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.

Quantitative analyses

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 quantitation 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.

Interaction proteomics

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 and 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.

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.

 

Fees

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.

Charging policy

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.

 

How and when to acknowledge the facility

Many users are not sure whether and how they should acknowledge the work done by core facilities and we would like to give some advice on this issue. Acknowledgements or co-authorships are important for core facilities as they provide an indication of the value of a facility and as such facilitate raising financial and further support in the future. The Association of Biomolecular Research Facilities (ABRF) has published a guideline (link), which we fully approve of and which we would also like to be the foundation of our interactions with users concerning this matter. In essence it says:

  • For routine analysis please mention the facility in the acknowledgement section of your manuscript.
  • If a faciliy team member develops novel resources or methods, contributes to the experimental design, or performs advanced data analyses which are an important part of the publication a co-authorship seems appropriate.

If you feel that this could become an issue just let us know as early as possible, ideally before the project starts, and we will certainly try to find a solution. In cases where co-authorship of a facility member might be warranted but is not an option to the user we also offer an additional data analysis service which is charged per hour.

back