Proteomics@PSL University

Proteomics@PSL Development of analytical strategies and last generation technologies for the life sciences and humanities such as archaeology and the environment. Proteomics@PSL has been an IbiSA-labelled platform since its creation. It brings together two very close sites, the Institut Curie and the ESPCI. Proteomics@PSL has been supporting researchers in their projects for more than 20 years. New analytical strategies have been developed in response to complex environmental and life sciences issues. When a disruptive technology appears, the platform transfers it to enrich its know-how and remain competitive. In 2002, she developed myProMS, a web interface for processing and sharing results (royalty-free software). In 2004, it was the first French academic site equipped with FTMS for proteomics. In 2014, it was the first to propose high-resolution proteomics and targeted strategies. In 2024, it is the first to offer high-throughput and high-sensitivity bottom-up proteomics in astral orbitrap mode, while preserving the high mass range and MALDI ionization at ESPCI and offering ion mobility at Curie. This has resulted in an increase in the number of users and the publication of more than 250 articles since 2013.

The structural and quantitative analysis of functional proteoforms and post-translational modifications now involves an effective combination of bottom-up, middle-down, and top-down approaches. Proteomics@PSL works globally, from the processing of the miniaturized sample to the bioinformatics processing of the data, which is validated on model samples.

In order to achieve an optimal level of specificity, sensitivity, throughput, and functionality for routine strategies on actual complex biological samples, a technology upgrade was undertaken in 2023-2024 to meet the current and future analytical needs of the scientific community for robust structural analysis of proteins and peptides. It allows us to offer a unique configuration in France, combining in the last configuration nanoESI Tribrid Eclipse with ultra-high resolution (1M), high mass range, reduction of state of charge, and ETD and UVPD fragmentations, with two nanoESI Astral orbitrap instruments working at high resolution and high analysis throughput while preserving extreme sensitivity. We also maintain the MALDI ionization mode at ESPCI with a TOF/TOF 5800, and ion mobility was recently acquired at Institut Curie with a TimsTOF Ultra. A project supported by PSL, ESPCI, Institut Curie, the cancéropole, and the Île-de-France region.

1. Sample processing for proteomics and peptidomics (proteolysis in solution, gel or raw tissue),
2. Identification, quantification of proteins, nanoLC MS/MS (TMT, iTRAQ, SILAC, label-free),
3. Phosphoproteomics, redox study, glycosylation at the peptide or protein scale,
4. Glycan mapping,
5. Identification of proteins after subcellular fractionation,
6. Analysis of whole proteomes,
7. Peptidomics and immunopeptidomics,
8. Analysis of biopsies and tissues,
9. Acquisition in DDA, DIA, or PRM modes,
10. Analysis in MALDI and ESI ionization mode,
11. Practical and theoretical training for scientists in immersion (one-week internships).

1. High-performance chromatography : 6 nanoRSLCs, 3 nanoLCs, and 1 UHPLC UV that can be coupled with mass spectrometry,
2. 6 high- or ultra-high-resolution ESI mass spectrometers : 2 Astral Orbitrap, 1 Tribrid Eclipse (ETD/UVPD), 1 Orbitrap Exploris 480, 1Q Exactive HF, 1Q Exactive,
3. MALDI TOF/TOF 5800 Mass Spectrometer,
4. Software tools for bioinformatics (myProMS, Mascot, Proteome Discoverer, Byonic, Peaks, Sequest, MaxQuant) and applied statistics (Perseus, R).

Direct contacts :

The facility has been labelled RIO National Proteomics Platform since 2001