Proteomics Platform


Proteomic Platform Proteomics Service Proteomic Research

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.

Relative protein quantification has become a powerful tool to decipher cell´s molecular basis and for that we use nLC MS/MS based Label Free quantification. Accordingly, we perform the relative quantification proteomic analyses with the recently acquired cutting-edge tims TOF Pro mass spectrometer, which is powered by PASEF (Parallel Accumulation Serial Fragmentation). Thanks to PASEF parent and fragment spectra can be aligned by mobility values achieving >100 Hz sequencing speed. This allows an unprecedented speed in data acquisition together with a very high sensitivity, enabling high performance proteomic analyses. The result is a straight forward analysis pipeline, letting us to get useful biological information starting from a very diverse type of samples: tissue samples, biological fluids, total cell lysates, exosomes, viruses etc.

Protein post-translational modification analysis is another field where mass spectrometry can be of great help. Our group has experience in the characterization of different PTMs by combining diverse sample preparation protocols and acquisition methods.

We have also settled in our laboratory the so called molecular histology by applying on tissue MALDI-TOF Imaging mass spectrometry.

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


The proteomics platform is equipped with a wide range of analytical instrumentation and also state of the art mass spectrometers.

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 Elute (Bruker) coupled on-line to a tims TOF Pro mass spectrometer (Bruker).

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


Besides, 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).

In addition, for tissue MALDI Imaging Mass Spectrometry studies, we make use of a prototype built in collaboration with IDEKO-IK4 for on tissue matrix spraying.

Service catalogue

The services offered by the platform are listed below.

  • Peptide Separation.
  • Protein and Peptide molecular weight analysis determination by MALDI-TOF.
  • Protein identification by nLC MS/MS.
  • 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. We will study different possibilities on how to tackle the analysis.

Service Request

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