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Mass Spectrometry

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Explore R&D Services

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


TripleTOF combined with SelexION™ Technology – SCIEX, model 6600

The SCIEX TripleTOF 6600 system is the top-performing TripleTOF in the market. It has a high-performance system with enhanced reproducibility, coupled to the Ekspert nanoLC 425 with micro and nano flow capabilities that can detect virtually every peptide in every run when executing SWATH Acquisition 2.0. It offers broader linear dynamic range (greater than 5 orders), wide Q1 mass range (isolation for ions up to 2250 m/z), enhanced mass accuracy stability, and superior mass resolution and speed (100 MS/MS per sec; 30,000 high-resolution TOF MS/MS mode).

Combined with SWATH Acquisition 2.0 it can deliver high-resolution quantification and rapid profiling.

The AB SCIEX SelexION™ Technology, especially in combination with mass spectrometry, has become a powerful separation tool, improving data quality in the quantitation and characterization of challenging biological samples. It can be used in a wide variety of applications in Omics research and biomarker discovery.

CESI – SCIEX, model 8000 Plus 

This is a versatile capillary electrophoresis (CE) instrument supplied with an ESI module with OptiMS technology. This system 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 the standalone set up, which becomes more reliable when coupled to MS detection:

  • 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 new compact system combines the Q-TOF high-resolution instrument and the HPLC, creating 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, or find new unspecified impurities in a single software.

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

The Q Exactive Focus mass spectrometer combines quadrupole precursor selection with 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. Its scan speed (up to 12 Hz) assures compatibility with fast chromatography and high-throughput screening.

The hybrid configuration allows the instrument to 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) for qualitative coverage of unknowns
  • Selected-ion monitoring (SIM) for highest sensitivity
  • Parallel-reaction monitoring (PRM) for high selectivity and high throughput

The system is connected to a Dionex Ultimate 3000 UHPLC to achieve micro flow analysis. This model can be applied to small molecules analysis, Omics research, namely metabolomics, and intact small protein analysis.

QTRAP – SCIEX, model 6500+

The Sciex QTRAP 6500+ merges triple quadrupole and linear ion trap technologies to create the world’s most sensitive triple quadrupole, with up to 10x increase in sensitivity and 20x increase in detector dynamic range, with no compromise in mass range. This performance results in low LODs and LOQs in complex matrices. Moreover, it delivers a remarkable linear quantification of up to 6 orders of magnitude.

Another important feature is the fast polarity switch which enables monitoring molecules in positive and negative mode in a single injection. The Sciex QTRAP has still an additional huge 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 – SCIEX, model 5800

MALDI-TOF/TOF is a high-throughput tandem time-of-flight (TOF) MS/MS system with soft ionization (MALDI – matrix-assisted Laser desorption/ ionization). In MALDI the analytes are co-crystallized with an organic matrix and then ionized by the action of a laser. This ionization source is coupled to a TOF mass analyzer including a reflectron for high-resolution separation of ions according to their mass/charge ratio and minimum mass accuracy of 50 ppm for masses under 3000 Da.

The MALDI-TOF/TOF is mainly used for protein identification, intact mass measurements, and purity profile determination. Additionally, it’s the ideal platform for mass spectrometry imaging.


A direct injection ion-trap that can be coupled to soft (ESI or nano ESI) or chemical (APCI) ionization sources.

The system is mostly useful for the determination of the molecular mass and fragmentation patterns of peptides, organic and organometallic compounds with a mass accuracy around 0.5 units.

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