Proteomics

The Proteomics Platform offers assessment and technology for the performance of studies ranging from small- or large-scale protein identification to the quantitative analysis of their level of expression, providing services to the sectors of biomedicine, systems biology, biotechnology or the chemical-pharmaceutical, cosmetics or food industries. It also develops its own projects in collaboration with third parties.

Services

  • Contract research projects (CRO).
  • Protein identification by means of enzymatic digestion and liquid chromatography coupled to mass spectrometry (LC-MS/MS).
    • Large-scale identification of proteins present in complex samples (cell extracts, biofluids, tissues).
    • Identification of proteins in single samples (polyacrylamide gel electrophoresis, purified proteins).
    • Protein complex characterisation. Identification of proteins present in a  complex (immunoprecipitation analysis, IP).
  • Post-translational modification analysis (PTMs) (LC-MS/MS).
    • Phosphorylation in purified proteins or complex samples (TiO2 enrichment is used for complex samples).
    • Acetylation, methylation, Gly-Gly in single samples.
    • Characterisation of isoforms in single samples.
  • Protein or phosphoprotein quantification (LC-MS/MS)
    • Quantification of proteins in complex samples by means of the label-free technique, with or without statistical analysis.
    • Protein quantification in complex samples by means of isobaric labelling techniques (iTRAQ or TMT) with or without statistical analysis.
    • Protein quantification in complex samples by means of isotopic labelling techniques (SILAC) with or without statistical analysis.
  • Targeted quantification (LC-MS/MS).
    • Optimisation of methods for quantifying proteins, peptides or metabolites during targeted mass spectrometry, PRM (parallel reaction monitoring).
    • Quantification of proteins, peptides and metabolites by PRM.
  • “De novo” peptide/protein sequencing
    • Identification of proteins not described in databases by means of LC-MS/MS and homology analysis.
    • Peptide sequence determination/confirmation by means of MS/MS.
  • Molecular mass determination
    • Determination of molecular mass of proteins/peptides/metabolites.
  • Molecular mass distribution by HPLC
    • Protein/peptide separation by GPC (gel filtration).
  • 1- or 2-D electrophoresis.
    • Protein separation by 2-D electrophoresis (2-DE).
    • Protein separation on polyacrylamide gels (SDS-PAGE).
    • Protein separation by isoelectric focusing (IPG strips).

Equipment

  • Mass spectrometers: Orbitrap Velos – ETD (Thermo Scientific), MALDI-TOF/TOF (ABSciex).
  • Liquid chromatographs : 2-D nanoUPLC system nanoAcquity (Waters) with dual pump system permitting 2D chromatography. 2D nanoUPLC system nanoEksigent (Eksigent) with dual pump system permitting 2D chromatography. HPLC Alliance system (Waters) with PDA detector (190-800 nm), automatic injector and oven with operating range of up to 80ºC. Empower Software. Ettan LC system (GE) with UV 900 detector, fraction collector and manual injector and Unicorn software.
  • Electrophoresis systems: Iso-Electric Focusing (IEF) – IPGphor system (GE) for strips of 7 to 21 cm. SDS-PAGE – Ettan Arriba II system (GE) and mini Protean system Mighly Small II (Hoefer) for gels of 20×24 cm and 7x 8 cm. ImageScanner and QuantityOne (BioRad) software for ice digitalisation.
  • Software: Mascot Server v2.3 (Matrix Science). Proteome Discoverer v1.4 (Thermo). PEAKS STUDIO 6.0 (Bioinformatics Solutions). Progenesis 2.0 (Waters). Skyline (MacCoss Lab free software). MaxQuant and Perseus (Jürgen Cox Group free software). R Statistics software (Free software by RStudio Team).

Member of the Spanish ProteoRed-ISCIII proteomics network, which is part of the platforms of the Instituto de Salud Carlos III: PRB3- Plataforma en Red de Recursos biomédicos [Networked Biomedical Resources Platform].

Other scientific services:

Experimental Toxicology and Ecotoxicology
Animal facility
Institutional Animal Care and Use Committee (IACUC)