Mass Spectrometry Unit

Introduction

The Mass Spectrometry Unit is a cross-disciplinary research support platform offering a range of services accessible to all researchers. Its mission is to drive, promote and carry out high-quality translational research by providing support in the fields of pharmacology, clinical research and proteomics.

Mass spectrometry is an analytical technique noted for its ability to identify and quantify a wide variety of molecules with great precision and sensitivity, even at extremely low concentrations (sub-femtomolar). Its high specificity allows for the differentiation of structurally similar compounds, whilst its multiplexing capability facilitates the simultaneous analysis of multiple analytes in a single injection.

The facility’s infrastructure combines micro-scale liquid chromatography with a hybrid triple quadrupole/linear ion trap mass spectrometer, enabling the identification and quantification of components with high sensitivity in a single analysis using DDA and MRM scanning techniques.

The range of services is available to staff from both the INCLIVA Foundation itself and other institutions, whether public or private.

Services

The services listed below may be requested with or without data analysis.

• Advice and methodological support in the drafting of protocols, research projects, articles, undergraduate/master’s dissertations and doctoral theses.
• Enzymatic digestion of samples from different biological matrices.
• Sample preparation for LC-MS via SPE purification.
• Protein characterisation by LC-MS peptide fingerprinting: MRM.
• Protein identification by LC-MS peptide fingerprinting: DDA.
• Data analysis using quantification software (Skyline and SciexOS).
• On-demand training in sample preparation protocols for both proteins and small molecules.
• Consultancy for projects based on mass spectrometry.

Equipment

• QTrap 6500+ hybrid LC-MS³ triple quadrupole mass spectrometry system with linear ion trap.
• Sciex M5 MicroLC high-precision micro-liquid chromatography system.
• SciexOS state-of-the-art data acquisition and processing software.
• Open-source software for reviewing quantification results, featuring a single interface for calibration curves, quantification data and spectra for peak reintegration, and the ability to programme MRM based on retention time (Skyline).
• Redundant storage system.

Quality

The quality and relevance of the services offered by the unit are evidenced by the fact that all sections within INCLIVA’s Core Facilities have held ISO 9001 quality certification since 2013 (certificate ES13/14611).

References of interest

García-Giménez JL, García-López E, Mena-Mollá S, Beltrán-García J, Osca-Verdegal R, Nacher-Sendra E, Aguado-Velasco C, Casabó-Vallés G, Romá-Mateo C, Rodriguez-Gimillo M, Antúnez O, Ferreres J, Pallardó FV, Carbonell N. Validation of circulating histone detection by mass spectrometry for early diagnosis, prognosis, and management of critically ill septic patients. J Transl Med. 2023 May 23;21(1):344. doi: 10.1186/s12967-023-04197-1.

Wienke J, Visser LL, Sánchez-Bernabéu A, Heck AJR, Koster J, Nierkens S, Janoueix-Lerosey I, de Krijger RR, Baryawno N, Chesler L, Anderson J, Caron HN, Margaritis T, van Noesel MM, Molenaar JJ. Integrative analysis of neuroblastoma by single-cell RNA sequencing identifies the NECTIN2-TIGIT axis as a target for immunotherapy. Cancer Cell. Feb 2024.

Mukherjee S., Sánchez-Bernabéu A., Demmers LC, Wu W, Heck AJR. The HLA Ligandome Comprises a Limited Repertoire of O-GlcNAcylated Antigens Preferentially Associated With HLA-B*07:02. Frontiers of Immunology. Dec 2021.

Ternette N, Block P, Sánchez-Bernabéu A, Borthwick N, Pappalardo E, Adbul-Jawad S, Ondondo B, Charles PD, Dorrell L, Kessler BM, Hanke T. Early kinetics of HLA class I-associated peptidome fo MVA.HIVconsv-infected cells. Journal of Virology. Mar 2015.

Mothe B, Manzardo C, Sánchez-Bernabéu A, Martínez-Picado J, Brander C, Hanke T. Therapeutic vaccination refocuses CTL responses towards conserved regions of HIV-1 in early treated individuals (BCN 01 study). EClinicalMedicine. Jun 2019.