Mass Spectrometry and Proteomics Facility

Activity

The Institut Curie Mass Spectrometry and Proteomics facility (LSMP) was established in 2001 to answer a request in proteomics. This service consists of personnel with specialized know-how and expertise in the proteomics field as well as state-of-the-art proteomics equipment (MS, LC, softwares, etc..).

New collaborators are met to discuss the most appropriate way forward in their project. Altogether, we design the experiment so as to answer their questions. Some biological and biomedical questions will apply existing technologies. Others are technically more challenging and require the development of new techniques, reagents or software in order to solve pressing problems.

Aims

The LSMP facility aims to provide researchers with technical services enabling them to analyze proteins (identification of proteins, comparison of proteomes, analysis of post-translational modifications, identification of partners interacting with the protein of interest etc.) by mass spectrometry. One of the most promising approaches is combining qualitative and quantitative analysis in a single analytical run (adapted to research samples, which means high sensitivity and low-level quantitation). The goal is to provide our collaborators with scientific hypotheses more quickly and to functionally validate our quantified candidates.

Networking

The LSMP facility is an “Ile-de-France Proteomics facility” for cancer research labeled IBiSA, which is part of the “Institut Curie / ESPCI” Montagne Sainte Geneviève Proteomic Facility. The LSMP is a founding member of Paris proteomics platforms network, is associated to the French Society for electrophoresis and proteomic analysis and to the French Society of Mass Spectrometry part of EuPA and HUPO.

Services

In practical terms, the facility carries out two distinct modes: collaborative or service. Fees are billed on an hourly basis for instruments usage.

  • Collaborative research requires advanced experiments by working closely in a true collaborative effort: a person of the research team is trained at the facility to prepare the samples and to interpret the data. The fees stand for machines maintenance contracts and consumables. Institut Curie subsidizes the rest.
  • Service: on each project, a service mode can be chosen if the co-signature is not wished. The analysis fees include people salary, structure costs and investments renewal.

The services provided:

  • Definition of optimal experimental design
  • Advice concerning the setting up
  • Advice and assistance in preparation of samples/quality control
  • Protein and peptide identification
  • Comparison of proteomes
  • Accurate mass measurements
  • Analysis of post-translational modifications (localization and characterization).
  • Targeted proteomics
  • Quantitative proteomics
  • MS processing
  • Bioinformatics and statistical analysis

Equipment

  • Thermo ScientificTM  Orbitrap FusionTM TribridTM MS
  • Thermo ScientificTM UltimateTM 3000 RSLCnano LC system
  • Thermo ScientificTM  DionexTM UltimateTM 3000 AFC Automated Fraction collector
  • AB SCIEXTM  TripleTOF® 6600 MS
  • AB SCIEXTM  4800 Plus MALDI TOF/TOFTM MS (2008, Applied Biosystems™)
  • Dionex/LC-Packings ProbotTM Micro Fraction Collector
  • Agilent 3100 OFFGEL Fractionator
  • Bio-Rad PROTEAN® IEF Cell
  • myProMS web server
  • Thermo ScientificTM Proteome DiscovererTM 2.0 software
  • Thermo ScientificTM PinpointTM 1.4 software
  • Database search algorithms (SEQUEST HT, Matrix Science Mascot Server and Daemon 2.5, AB SCIEX ProteinPilot 5.0, …)
  • AB SCIEXTM  PeekView® 2.1 software
  • Trans-Proteomic Pipeline (TPP 4.8) tools

 

Training and methodological expertise

The LSMP Facility aims at providing to its users three types of expertise: 1-personalized training to realize a part of analyses; 2-advanced training about all aspects of Proteomics (from helping in defining questions and experimental design, to sample preparation, through MS analysis, to MS processing and analysis); 3-development of MS processing and analysis tools.

The LSMP develops in-house solutions, in collaboration with the Bioinformatics platform (U900), to provide the community with bioinformatical tools for management, mining, curation or mass spectrometry-based (MS) data sharing. The web server myProMS was designed to handle projects and curate databank-search results from multiple MS runs while optimizing data sharing between users with complementary competences. It is improved continuously so as to be up-to-date with the quality standards. myProMS is a freely distributed tool, GPL license, already implemented in 4 institutes (ESPCI, Institut Cochin, IGF de Montpellier and IC).

 

Manager and Team

The LSMP facility is managed by Damarys Loew and has a team specialized in the field of 1) Mass spectrometry and proteomics 2) Biology and 3) Bioinformatics

  • Dr Damarys Loew, mass spectrometry specialist and facility manager contact: Tél. : +33 (0)1 56 24 65 22 ()
  • Bérangère Lombard, MS engineer
  • Florent Dingli, Proteomic engineer
  • Guillaume Arras, Bioinformatic engineer
  • Vanessa Masson, Biology engineer
  • Marine Le Picard, Bioinformatic engineer

Key publications

Year of publication 2016

Lisa Prendergast, Sebastian Müller, Yiwei Liu, Hongda Huang, Florent Dingli, Damarys Loew, Isabelle Vassias, Dinshaw J Patel, Kevin F Sullivan, Geneviève Almouzni (2016 Jun 11)

The CENP-T/-W complex is a binding partner of the histone chaperone FACT.

Genes & development : 1313-26 : DOI : 10.1101/gad.275073.115
Joanna Kowal, Guillaume Arras, Marina Colombo, Mabel Jouve, Jakob Paul Morath, Bjarke Primdal-Bengtson, Florent Dingli, Damarys Loew, Mercedes Tkach, Clotilde Théry (2016 Feb 8)

Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes.

PNAS : 113: E968-977 : DOI : 10.1073/pnas.1521230113

Year of publication 2015

Gentili M, Kowal 1, Tkach M, Satoh T, Lahaye X, Conrad C, Boyron M, Lombard B, Durand S, Kroemer G, Loew D, Dalod M, Théry C, Manel N. (2015 Jul 30)

Transmission of innate immune signaling by packaging of cGAMP in viral particles.

Science : DOI : 10.1126/science.aab3628
Ewa Kotula, Nathalie Berthault, Celine Agrario, Marie-Christine Lienafa, Anthony Simon, Florent Dingli, Damarys Loew, Vonick Sibut, Simon Saule, Marie Dutreix (2015 May 29)

DNA-PKcs plays role in cancer metastasis through regulation of secreted proteins involved in migration and invasion.

Cell cycle (Georgetown, Tex.) : 1961-72 : DOI : 10.1080/15384101.2015.1026522
Guillaume Kellermann, Markus Kaiser, Florent Dingli, Olivier Lahuna, Delphine Naud-Martin, Florence Mahuteau-Betzer, Damarys Loew, Evelyne Ségal-Bendirdjian, Marie-Paule Teulade-Fichou, Sophie Bombard (2015 May 11)

Identification of human telomerase assembly inhibitors enabled by a novel method to produce hTERT.

Nucleic acids research : e99 : DOI : 10.1093/nar/gkv425
Mercè Guzmán-Vendrell, Sergio A Rincon, Florent Dingli, Damarys Loew, Anne Paoletti (2015 Apr 17)

Molecular control of the Wee1 regulatory pathway by the SAD kinase Cdr2.

Journal of cell science : 2842-53 : DOI : 10.1242/jcs.173146
All publications