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CRG/UPF Proteomics Unit

The Proteomics Unit is a joint effort of Universitat Pompeu Fabra and the Center of Genomic Regulation to create an innovative core facility that provides high quality proteomics services to its final users, by providing proper expertise and advice, and by developing new methods and techniques.

The Proteomics Unit provides full service in a variety of proteomics applications including protein quantification, identification of post-translational modifications, and data analysis, among others. In addition to the services provided to the research community, the Proteomics Unit also promotes internal technology-driven research as an essential task to keep the unit at the forefront of the proteomics field.

The Proteomics Unit is part of the "Plataforma de Recursos Biomoleculares y Bioinformáticos (ProteoRed, Instituto de Salud Carlos III)".

 

Services

Protein-protein interactions

  • Setting up of a protein-protein interaction experiment (IP, AP-MS)

  • Characterization of protein-protein interactions (IP, AP-MS)

Post-translational modifications

  • Acetyl, methyl, Gly-Gly PTM identification and quantification of a purified protein (LC or IP)

  • Identification and quantitation of post-translational modifications in purified histones.

  • Quantitation of post-translational modifications in purified histones.

  • Phosphorylation PTM identification of a purified protein (LC or IP)

Label-free (phospho-)proteome quantitation

  • Label-free protein quantitation in complex samples with and without statistical analysis

  • Label-free phosphopeptide quantitation in complex samples with and without statistical analysis

Label-based (phospho-)proteome quantitation

  • Protein quantitation in complex samples by SILAC with and without statistical analysis

  • Protein quantitation in complex samples by iTRAQ with and without statistical analysis

  • Protein quantitation in complex samples by TMT with and without statistical analysis

  • Phosphopeptide quantitation in complex samples by SILAC with and without statistical analysis

Single-protein analysis

  • Confirmation of an overexpressed protein in complex samples

  • Identification of a protein in a gel band.

  • Molecular weight determination of intact protein

Targeted Proteomics

  • Peptide selection for targeted proteomics quantitation with SRM

  • Optimization of SRM methods for targeted protein quantitation

  • Targeted protein quantitation with SRM with and without statistical analysis

  • Peptide selection for targeted proteomics quantitation with PRM

  • Optimization of PRM methods for targeted protein quantitation

  • Targeted protein quantitation with PRM with and without statistical analysis

  • Peptide selection for targeted proteomics quantitation with DIA

  • Optimization of DIA methods for targeted protein quantitation

  • Targeted protein quantitation with DIA with and without statistical analysis

 

Equipment

As a reference proteomics center, the Proteomics Unit has state-of-the-art equipment consisiting on high resolution liquid chromatography and electrophoresis systems, and four advanced mass spectrometers to identify and quantify the proteins of interest.

The instruments available at the Proteomics Unit cover the most advanced techniques of the proteomics field, and are accessible to national and international scientists.

Mass spectrometers

  • LTQ-Orbitrap Fusion Lumos (Thermo) Purchase year: 2015.

  • Q-TOF 5600 (Sciex). Purchase year: 2013.

  • Q-Trap 5500 (Sciex). Purchase year: 2011.

  • LTQ-Orbitrap Velos Pro (Thermo). Purchase year: 2010.

  • LTQ-Orbitrap XL (Thermo). Purchase year: 2008.

Chromatographic systems

  • 1x Nano-HPLC chromatographic equipment (Agilent)

  • 2x Nano-HPLC chromatographic (Eksigent)

  • 3x Nano-HPLC chromatographic (Thermo Proxeon)

  • 1x Micro-HPLC chromatographic equipment (Agilent)

Computer resources

  • HP Server X5660 DL360G6/G7 (2xCPU, 12 cores, 64 GB RAM).

  • ProLiant BL460c Gen9 (2xCPU E5-2690 v4, 28 cores, 64 GB)

Software suites and packages

  • Mascot Server v2.4 (Matrix Science).

  • Proteome Discoverer v2.1 (Thermo).

  • PEAKS 7.0 (Peaks).

  • Progenesis 2.0 (Waters)

  • Open Source packages installed as part of the data analysis pipeline: Transproteomics Pipeline, OpenMS 1.9, PeptideShaker, OMSSA, XTandem.

 

Service Prices

Proteomics Unit Prices

 

Personnel

Cristina Chiva

Eva Borràs

Guadalupe Espadas

Roger Olivella

Amanda Solé

Olga Pastor

Mireia Ortega

Melissa Bradbury

Daniel Mancera

Julia Morales