Proteomics

Using proteomics as a study tool, we can better understand translational medicine and help develop personalized medicine.

The Proteomics Unit of IDIBELL provides scientific and technological support to IDIBELL researchers and external ones in different areas.

Our technical staff has extensive experience in experimental design, analysis of sample preparation, analytical workflows, bioinformatic data mining and visualization, drafting of projects and manuscript preparation.

The Unit collaborates with the proteomic platform of the Parc Científic de Barcelona (PCB) and has access to the latest generation equipment in collaboration with external organizations.

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 

Equipment -  colaboration with external organizations

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.

Certifications 
IDIBELL Proteomics Units belongs to the Spanish “Plataforma de Recursos Biomoleculares y BioinformáticosPrograma de Proteómica” (ISCIII AES-2013-PRB2) and the Spanish Human Proteome Project Chr 16 Consortium (SpHPP) (targeted proteomics S/MRM and sequencing groups), an initiative of the Human Proteome Project.