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Mass Spectrometry

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At iBET we provide state-of-the-art Mass Spectrometry services, guaranteed by a continuous increase in know-how and infrastructures within our Mass Spectrometry Unit (UniMS)

Our Mass Spectrometry services are part of iBET’s Analytical Services Unit (GMP certified by INFARMED, the Portuguese branch of EMA), and it is also a node of the Portuguese Mass Spectrometry Network (RNEM)

Mass Spectrometry Services

  • Protein/peptide Identification – Proteomics
  • Antibody Characterization – MAM
  • High-throughput Quantitative Proteomics – SWATH analysis, MRM-HR and label-based quantification (e.g. iTRAQ)
  • Intact Protein Characterization
  • Small Molecule Mass Characterization 
  • Small Molecule Identification & Quantification – Metabolomics


TripleTOF combined with SelexION™ Technology – SCIEX, model 6600


The SCIEX TripleTOF 6600 mass spectrometer is coupled to the EkspertnanoLC 425 with micro and nano flow capabilities. This high-performance system offers broader linear dynamic range, wide Q1 mass range, enhanced mass accuracy stability, and superior mass resolution and speed (30,000 high-resolution TOF MS/MS mode). Combined with SWATH Acquisition 2.0 it can deliver high-resolution quantification and rapid profiling, virtually detecting every peptide in the sample. The SCIEX SelexION™ Technology improves data quality in the quantitation and characterization of challenging biological samples.

CESI – SCIEX, model 8000 Plus 

sciex 8000

This capillary electrophoresis (CE) instrument can be used as a standalone or in conjunction with the mass spectrometer (TripleTOF 6600), achieving enhanced sensitivity and coverage with the ultra-low flow (<10 nL/min). Small sample amounts can be injected, down to the nanoliter range, or a specific set of charged molecules can be injected through electrokinetic injection. There is a variety of information that can be obtained from this equipment, namely:

•Proteoforms & peptide PTMs such as those with multiple phosphorylation sites;
•Intact mAb charge variants;
•Native protein conformation and interactions under native conditions;
•Isobaric metabolites and glycans;
•Challenging charged & polar metabolites/degradation products such as anionic and/or hydrophilic analytes.

QTOF – SCIEX, model X500B


This compact Q-TOF high-resolution system is a true benchtop platform capable of high-throughput intact mass analysis and peptide mapping. The association with the intuitive SCIEX OS platform and BioPharmaView™ Software makes this system especially suited for biologics characterization. Its tools enable a complete Multiple Attribute Methodology (MAM) Workflow, that allows defining, tracking and quantifying product quality attributes as well as specified contaminants (incl. HCP analysis), or find new unspecified impurities in a single software.

Q Exactive™ Hybrid Quadrupole-Orbitrap™ Mass Spectrometer – ThermoFisher, Focus model 

q executive -thermofisher

This mass spectrometer combines quadrupole precursor selection with ultra high-resolution (70,000 at m/z 200) analysis to produce high-sensitivity and accurate-mass detection, a wide linear dynamic range and confident identification. The fast polarity switching enables the processing of more classes of compounds in a single analysis. This instrument can perform both targeted and untargeted screening, in a number of quantification approaches, including:

• Full-scan – data-dependent MS/MS (FS-ddMS2) acquisition (Top3)
• Variable data-independent acquisition (vDIA)
• Selected-ion monitoring (SIM)
• Parallel-reaction monitoring (PRM).
This UHPLC-MS system facilitates Omics research, namely metabolomics.

QTRAP – SCIEX, model 6500+

qtrap sciex

The Sciex QTRAP 6500+ merges triple quadrupole and linear ion trap technologies to obtain increased levels of sensitivity and detector dynamic range. This performance results in low LODs and LOQs in complex matrices, and a remarkable linear quantification of up to 6 orders of magnitude.

The fast polarity switch enables monitoring molecules in positive and negative mode in a single injection. The Sciex QTRAP has an additional advantage in selectivity: the ability to achieve MS/MS/MS (or MRM3) quantification by selecting and quantifying the fragment of a fragment ion.

MALDI-TOF/TOF Mass Spectrometer – SCIEX, model 5800

maldi tof tof

This system is a high-throughput tandem time-of-flight (TOF) MS/MS system with soft ionization (matrix-assisted laser ionization). This ionization source is coupled to a TOF mass analyzer including a reflectron for high-resolution mass measurements.

The MALDI-TOF/TOF is mainly used for:
•Protein identification 
•Intact mass measurements up to 100.000 Da
•Purity profile determination

ION TRAP Mass Spectrometer – BRUKER, model ESQUIRE 3000+

ion trap

A direct injection ion-trap that can be coupled to soft ionization source (ESI). The system is mostly useful for the determination of the molecular mass and fragmentation patterns of organic and organometallic compounds with a mass accuracy around 0.5 mass units.

Assay Request

Please fill our Assay Request Form (v2.2) and send it to when sending your samples to us.


All services provided by the UniMS should be acknowledged in scientific publications with the following sentence: “MS data were generated by the UniMS – Mass Spectrometry Unit, iBET/ITQB, Oeiras, Portugal”.

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