Proteomics Platform


Our aim In Proteomics Platform at CIC bioGUNE is to provide high quality standards on proteomic analysis to anyone interested. Since we are aware that proteomics is much more than just protein identification, we foster the development and settling of new proteomic technologies and methodologies. Lately we have been focusing our efforts on improving and expanding the portfolio of analytical techniques offered so we can add our little contribution to the ambitious endeavor of understanding the complexity of the proteome.

Since one of the more frequent analysis petitions is the relative protein quantification, we have moved from labeling methods (DIGE and iTRAQ) to Label Free quantification based on nLC MS/MS generally using Progenesis IQ software. The result is a cheaper service and straighter forward analysis pipeline. By applying this methodology we achieve high quality results in our analysis (e.g. Gomez-Sanchez J.A. et al. J Cell Biol, 2015).

With the aim to settle the so called molecular histology, where peptide spatial information is achieved in tissue sections, we developed together with IDEKO-IK4 a MALDI matrix nebulizer.

With the aim to settle the so called molecular histology, where peptide spatial information is achieved in tissue sections, we developed together with IDEKO-IK4 a MALDI matrix nebulizer.

Preliminary data shows that the prototype is highly competitive (Iloro et al. J Lab Autom. 2015)

Another example of new development is the efforts we have done settling the methodology for endogenous peptide identification by nLC MS/MS. In collaboration with a neighbor company Bioftalmik Applied Research, we applied the strategy to accomplish the largest naturally occurring human tear peptidome, proving that some identified peptides show antibacterial activity (Azkargorta et al. J Proteome Res 2015).

Proteomics Platform at CIC bioGUNE is integrated in the ProteoRed-ISCIII Spanish Proteomics Services Network


The proteomics platform is equipped with a wide range of analytical equipment and also state of the art mass spectrometry instrumentation. We have a Typhoon scanner, spot picker and all electrophoresis equipment needed for DIGE analysis. We have a nano scale chromatographer (Agilent 1100) coupled to a probot (LC-Packings); for preparative peptide separation at microgram scale we have a chromatographer (Agilent 1100) with UV detector and sample collector and different columns (e.g. High pH Reverse Phase, Hydrophilic Interaction Liquid Chromatography-HILIC); for MALDI Imaging Mass Spectrometry we make use of a prototype built in collaboration with IDEKO for on tissue matrix spraying. For protein characterization, identification and quantification, we have three mass spectrometers.

  • Autoflex Smartbeam MALDI TOF (Bruker).
  • Nano Acquity (Waters) coupled on-line to an Orbitrap XL ETD mass spectrometer (Thermo).
  • Nano Acquity (Waters) coupled on-line to a Synapt G2Si mass spectrometer (Waters).

These mass spectrometers are highly complementary and allow us to prove a very wide range of proteomic analysis (see Service Catalogue).

Service catalogue

The services offered by the platform are listed below.

  • Peptide Separation.
  • Protein Molecular weight analysis determination by MALDI-TOF.
  • Peptide and protein profiling solid Phase Extraction MALDI-TOF.
  • Protein identification.
  • Protein relative quantification by label free nLC MS/MS.
  • Protein Characterization: Post-translational Modification analysis*.
  • Tissue MALDI Imaging Mass Spectrometry*.
  • Natural Peptidome (endogenous peptides) analysis by nLC MS/MS.

*Contact Platform Manager for more information about these services. Please, do not hesitate contacting us if you would require a service which is not listed so we will check different possibilities on how to tackle the analysis.

Service Request

For information about experimental design and quote contact directly Felix Elortza through our dedicated tool link