CFMP Core Facility for Mass Spectrometry & Proteomics

• Analysis of post-translational modifications (e.g. phosphorylation, succinylation)
• Identification of cross-linked peptides of purified proteins and protein complexes
• Cell-wide or organelle-wide interactome analysis (co-fractionation MS)
• Please, contact us for additional application that may fit your needs.

• Please, familiarize yourself with the recommendations on sample preparation appropriate for the chosen service and sample submission guideline. Before submitting a request, please schedule an appointment with Marcin Luzarowski: 

  m.luzarowski@zmbh.uni-heidelberg.de

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• Details about sample submission can be found here: 

  Link

• Each facility user is obliged to be familiar and sign CFMP user regulations. 

  Link

• The contribution of the CFMP to the research projects should be appropriately acknowledged. It helps CFMP to be recognized and ease applications for external funding and the acquisition of new instruments. As scientific contribution can be considered:
• Development of new analytical method
• Help with experimental design
• Generation and/or evaluation of the data
• Manuscript preparation, generation of figures, supplementary data preparation and raw data submission
• Samples are processed on a first come first serve basis. Sample processing includes protein digestion into peptides, sample clean-up, peptide separation and quantification using LC-MS and initial database search. Regular services are processed usually within 2-4 weeks. Additional services usually take up to 8 weeks.
• Detailed price list including project examples can be found here [link]. Please, note that the final price has to be discussed with the head of the CFMP.

Acknowledgment: We extend our gratitude to our colleagues at EMBL for engaging discussions on website organization and generously sharing informative content from their website.

• Molecular weight determination of intact proteins 

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• Protein identification of gel separated proteins 

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• Identification of interaction partners from Co-IP experiments 

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• Analysis of proximity labeling (BioID) experiments 

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• Proteome analysis 

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General guidelines and practical hints relevant for sample preparation

• Contaminants may be introduced at several steps during sample preparation. Some will go unnoticed, others will totally obscure all proteins. Therefore, minimizing contamination is essential.
• Keratins are omni-present and notorious contaminating proteins originating from skin, hair, dust, clothes, chemicals, etc. Total elimination is virtually impossible (and not necessary), but over-abundance will result in the repeated identification of keratins, and not your protein of interest. Most contaminating keratins originate from dust collected during sample processing. Therefore, a clean lab environment will certainly benefit the outcome of the MS experiment. To reduce keratin contamination, use clean containers for staining gels, cover them with a transparent plate when inspecting them and bind your hair.
• Other frequently observed proteins are BSA, immunoglobulins, and other serum proteins. These usually originate from cell culture media, and can be reduced by extensive washing of cell pellets with PBS prior the lysis/ protein extraction.
• In a way, polymers are more serious contaminants than keratins, since they tend to stick to HPLC columns either ruining them, or at least causing a severe memory effect in subsequent LC-MS runs. On top of this, most polymers ionize more easily than peptides ─ so that even minute amounts can be deleterious for the experiment. The most frequently observed polymers are various forms of PEG, which are present in some plastics but also in soaps, hand-creams (wear gloves!) and detergents. Don`t perform additional autoclaving of tubes or tips because that may release plasticizers which interfere with the downstream analysis.
• One of the most pivotal steps in sample processing is the preparation of cell lysates or protein precipitates. To do that in a reproducible way is a difficult task. Imagine that you are working with thousands of proteins with very different properties and a proteomics analysis aims to accurately quantify all of them.
• Variability in protein extraction is a major cause of low-quality proteomics data. Always try to use protocols which are as simple as possible to increase reproducibility. We recommend to optimize your sample preparation before preparing your sample for Proteomics.
• Sample quality, protein amount and protein extraction reproducibility can be checked using colorimetric assays for protein concentration determination, SDS PAGE/Coomassie staining and Western blotting. If suitable antibodies are available, western blotting can be used to confirm presence of a protein of interest (e.g. bait protein) in the samples before submitting them to the facility.