The MS Proteomics Unit Biology of Plants (MSPUB)
The Mass Spectrometry-based Proteomics Unit Biology of Plants (MSPUB) performs large scale proteomic analyses for all research groups at the IBBP. We provide a versatile proteomics platform including sample digestion, mass spectrometry, and data analysis. Our expertise includes:
- Identification of single proteins for quality control (e.g. recombinant proteins)
- Identification and quantification of proteins in complex proteomes; relative and absolute quantitations are feasible
- Quantitative analysis of post-translational modifications of proteins (e.g. phosphopeptide enrichments)
- Protein pull-downs and interaction studies
The core instruments of our facility include three mass spectrometers which are used in dependence on the sample requirements:
- QExactive Plus, hybrid quadrupole-Orbitrap (Thermo Scientific)
- QExactive HF, hybrid quadrupole-Orbitrap (Thermo Scientific)
- LTQ Orbitrap (Thermo Scientific)
We use several bioinformatic tools to analyse large proteomic datasets including ProSight, Proteomatic, pyQms, Skyline and MaxQuant in conjunction with Perseus for statistical analysis. Analysis reports are provided in Excel format. Data from collaboration projects is archived on local servers and researchers can be granted access to raw data upon request.
Before you start a project:
As there is no universal proteomics workflow, and experiment design and sample preparation are very important, it is mandatory to contact our facility for consulting before you start a project.
General guidelines for protein extractions:
- Work in a clean environment, protect sample from skin /wool keratin and dust
- Wear gloves, close tubes, tip boxes after use
- Keep sample storage and processing time as short as possible
- Keep sample on ice if non-denaturing buffer is used and use MS compatible protease/phosphatase inhibitors.
- Sample solutions must not contain polymers, like PEG. Also, samples in solution must be free of the following detergents (and their derivatives): NP40, Tween 20, Triton X-100, Brij-35.
- Use high quality, low binding and non-autoclaved plasticware
- Measure protein content (usually 10- 50 µg of protein extract is required, for PTM enrichments even up to mg amounts)
- Avoid longer storage of samples in fridge, freeze proteins if it needs to be stored for more than a day
For collaborative projects, any intellectual input from our scientific members into the project during planning, execution and analysis of the experiments justifies a co-authorship on a manuscript that contains data generated in our facility.
User Regulation of MSPUB
The detailed user regulation including pricing can be downloaded here.