Mass Spectrometry

Quantification

Our pipelines support quantitation of peptides and proteins, using metabolic (SILAC) or chemical (e.g. 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.

For more information concerning sample submission and sample preparation please have a look at our guidelines here.

Interaction proteomics

Protein affinity enrichment followed by mass spectrometry has become a major technology for determining protein interactors. In our workflow we apply label-free quantification to distinguish between background proteins and true interactors. If performed in sufficient replicates this allows comparative statistical analysis to define interaction partners with higher confidence.

For more information concerning sample submission and sample preparation please have a look at our guidelines here.

Cross-linking 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. We offer a specialised workflow for your cross-linked protein samples including digestion in gel or in solution, LC-MS/MS measurement, and data analysis.

For more information concerning sample submission and general sample preparation please have a look at our guidelines here.

For cross-linking specific guidelines please follow the link here.

Please note that this service is only available to groups from Max Perutz Labs, University of Vienna, and Medical University of Vienna.

Intact protein mass analysis

Determining the mass of an intact protein as accurately as possible can 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.

For more information concerning sample submission and sample preparation please have a look at our intact protein MS guidelines here.

Please contact proteomics@maxperutzlabs.ac.at 

We have shared access to the following instruments which are owned and maintained by Vienna Biocenter Core Facilities (VBCF):

• Thermo Exploris 480

• Thermo Eclipse

• Bruker timsTOF HT

• Waters Synapt G2-Si HDMS

Most of the mass spectrometers are coupled to Thermo Scientific Vanquish Neo systems for reliable, high performance separation of the samples. For more detailed information on the different instruments please visit the website of the VBCF.

Based on the application and the research question we apply different software packages and search engines. Currently these include FragPipe, MaxQuant, Spectronaut, pLink, Merox, and Skyline. For downstream statistical analysis we use Perseus, Python and R. All scripts developed in house and custom scripts for publications are released on our GitHub-repository.

Acknowledgements or co-authorships are very important for core facilities as they facilitate raising funds and support in the future. For this reason we request acknowledgement for the use of the facility services in your publications according to the following logic:

• For routine analysis we kindly ask you to mention the facility (as "Max Perutz Labs Mass Spectrometry Facility") in the acknowledgement section of your manuscript. 
  
  A suggested minimum format would be: 
  “Proteomics analyses were performed by the Mass Spectrometry Facility at Max Perutz Labs using the VBCF instrument pool.”

• If a service was provided through the Vienna Life Science Instruments Initiative (VLSI) please add “a member of VLSI” after “Max Perutz Labs”.

• If a facility team member develops novel resources or methods, contributes substantially to the experimental design, or performs advanced data analyses which are beyond the invoiced routine service and which are an important part of the publication a co-authorship seems appropriate.
  
  This policy is also suggested by the Association of Biomolecular Research Facilities (ABRF) which has published a guideline on this matter. If you think that this could become an issue just let us know as early as possible, ideally before the project starts, and we will try to find a solution.