Available Services

This service comprises 8 hours of equipment time on the Orbitrap Astral LC-MS. The configuration of the system is: Vanquish NEO HPLC in trap and elute configuration. Mobile phase A is 0.1% formic acid in water, mobile phase B is 80% acetonitrile in water with 0.1% formic acid. The MS is set up with an EasySpray source. The MS is operated for high- throughput, with EasySpray pepMap columns (15cm, 150µm diameter, 10nm pore size). It is possible to use the FAIMS filter to improve sensitivity or fractionate samples online. Overhead on measurements due to sample loading and column washing is about 2 minutes per injection. Typical gradient length 15 minutes (no gains are typically observed beyond this gradient length due to the speed of the Astral analyser and the operation in high flow). This configuration allows for up to 100 samples per day. Both DIA and DDA proteomics workflows are available.  The service does not comprise sample preparation from proteins to peptides.

This service comprises 8 hours of equipment time on the Orbitrap Astral LC-MS. The configuration of the system is: Vanquish NEO HPLC in trap and elute configuration. Mobile phase A is 0.1% formic acid in water, mobile phase B is 80% acetonitrile in water with 0.1% formic acid. The MS is set up with an EasySpray source. The MS is operated for high- load, using EasySpray pepMap NEO columns (50cm, 75µm diameter, 10nm pore size). It is possible to use the FAIMS filter to improve sensitivity or fractionate samples online. Overhead on measurements due to sample loading and column washing is about 10 minutes per injection. Typical gradient length 30 minutes (no gains are typically observed beyond this gradient length due to the speed of the Astral analyser). Both DIA and DDA proteomics workflows are available. Each proposal can request up to 9 sessions for a total of 3 days of MS time. The service does not comprise sample preparation from proteins to peptides.

The Structural Proteomics unit will perform integrative structural modelling combining medium/ low resolution (from 7 to 30 Å) cryo-EM densities and crosslinking MS data acquired at our NF. In case of very large systems, negative stain data may also be used. This does not refer to model building in cryo-EM densities, but to calculations of localization of subunits or of areas not observed in EM maps. This task can be performed on data from services SB-IU4-A or SB-IU4-B only. Example software: DisVis, integrative modelling platform (IMP), AlphaLink/ AlphaLink2. This service will be performed by NF staff, but training will be available if requested, provided basic bioinformatics skills of the User (bash terminal, python).

The Structural Proteomics unit will perform crosslinking MS on a purified protein complex to identify protein-protein interactions and map residue distances. This service does not include preliminary crosslinking reaction optimisation, which should be performed by the User at their own institution (in consultation with NF staff). This service will only be performed by NF staff.

The Structural Proteomics unit will perform crosslinking MS on a purified protein complex to identify protein-protein interactions and residue distances. This service includes preliminary crosslinking reaction optimisation and proteomics acquisitions. These can be performed by our NF staff provided the protein sample, or by a visiting User with our assistance.

The Structural Proteomics unit will perform crosslinking MS to characterize the interactome of a particular target protein in situ. Crosslinking reactions can be performed on cells, in lysate or after competitive or otherwise non-denaturing (native) elution. As this experiment requires a careful and at times tricky design, preliminary results will be shared with the User and guidance provided to set or optimize the experimental conditions. This service will be performed by NF staff if the crosslinking reaction occurs at the home institution with guidance from us, or by a visiting User under our direct supervision if the entire workflow is requested.

The Structural Proteomics unit will perform crosslinking MS to characterize the topology of the protein-protein interactome of a particular target protein or enriched cellular fraction in situ. Examples include: interactome of pulldowns with an endogenously tagged protein of interest; interactome of vesicles/ cellular compartments; interactome of bacterial cells or virus/ host interactions after pulldown of specific virulence factors. Crosslinking reactions can be performed on cells, on lysates or after competitive or otherwise non-denaturing (native) elution. As these experiments require careful design, the User will be granted Access to preliminary acquisitions to characterise the sample and set the correct reaction conditions, or guidance to perform the optimization at their home institution. This service will be performed by NF staff in collaboration with a visiting User.