Mass Spec Facility UniMS

High-Throughput Proteomics Profiling

(including PTM Characterization and Biomarker Profiling)

– ZenoTOF 7600

– TripleTOF 6600

High-Throughput Quantitative Proteomics

(SWATH analysis, MRM-HR, and iTRAP)

– ZenoTOF 7600

– TripleTOF 6600

High-Resolution Small Molecule Mass Measurement

– Orbitrap Q Exactive Focus

Proteins/Peptides Identification

– TripleTOF 6600

– QTOF X500B

– MALDI-TOF/TOF 5800

Small Molecule Semi-Quantification (Non-target)

– Orbitrap Q Exactive Focus

– QTRAP 6500+

Small Molecule Identification (Non-target)

– Orbitrap Q Exactive Focus

– QTRAP 6500+

Protein Intact Mass Measurement

– TripleTOF 6600

– QTOF X500B

– MALDI-TOF/TOF 5800

Small Molecule Quantification (Target)

(Vitamins, Organic Acids, Sugars, Amino Acids, and more)

– Orbitrap Q Exactive Focus

– QTRAP 6500+

Characterization of Antibodies

(Multiple Attribute Methodology)

– TripleTOF 6600

– QTOF X500B

– CESI 8000 Plus

Fragmentation Profile (MSⁿ)

– MALDI-TOF/TOF 5800

– All ESI-MS

Polymers Intact Mass Measurement

– MALDI-TOF/TOF 5800

Product Stability and Impurity Analysis

(incl. Host Cell Protein (HCP) Analysis)

– QTOF X500B

– LCQ and ESQUIRE

ZenoTOF SCIEX, 7600 model

The ZenoTOF 7600 system is an accurate mass spectrometry solution that combines powerful MS/MS sensitivity, innovative fragmentation technology, and a step-change in data-independent acquisition (DIA). The Zeno trap enables MS/MS sensitivity gains by overcoming QTOF MS/MS duty cycle deficiencies. The Zeno SWATH-DIA delivers a high depth of coverage, particularly on low-abundance species. Besides collision-induced dissociation (CID) fragmentation, the ZenoTOF 7600 includes tunable electron activated dissociation (EAD) fragmentation which allows a deeper product characterization, from singly charged small molecules to large multiply charged proteins.

TripleTOF combined with SelexION™ Technology SCIEX, 6600 model

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

QTOF SCIEX, X500B model

This compact QTOF 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, BioPharmaView™ and Biologics Explorer™ Software makes this system especially suited for biologics characterization. It enables a complete Multiple Attribute Methodology (MAM) Workflow, that allows defining, tracking, and quantifying product quality attributes as well as specified contaminants (including Host Cell Protein (HCP) analysis) or finding new unspecified product impurities.

QTRAP SCIEX, 6500+ model

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

CESI SCIEX, 8000 Plus model

This capillary electrophoresis (CE) instrument can be used as a standalone or coupled with the mass spectrometer (TripleTOF 6600), with the ESI module and OptiMS technology, 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 post-translational modifications (PTMs) such as those with multiple phosphorylation sites; Intact monoclonal antibodies (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.

Orbitrap™ Q Exactive™ Hybrid Quadrupole ThermoFisher, Focus model

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

MALDI TOF/TOF SCIEX, 5800 model

This system is a 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 from SDS-PAGE or 2D-gel electrophoresis. And allows for ESI-complementary sample analysis and mass spectrometry imaging.

API-ION TRAP ThermoFisher, LCQ model

This is an ion trap mass analyzer can be used for sample direct infusion or coupled (on-line) to an HPLC system for previous separation of complex samples. The LCQ can use soft-(ESI) or hard-ionization (APCI). This MS system is mainly used for molecular mass and fragmentation pattern determination of proteins, peptides, organic and organometallic compounds.

API-ION TRAP BRUKER, ESQUIRE 3000+ model

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. Our LC-MS systems operate in nano, micro, or analytical flows, we have both MALDI and ESI electrospray sources, and can explore CID or EAD fragmentation, depending on the equipment selected, making our workflows highly adaptable to a wide range of analytical challenges.

The Mass Spec facility serves ITQB NOVA researchers (see pricing table here) as well as external users. Please see the contacts below for more information.

Both the purchase order and the assay request form are mandatory to start sample processing. Analysis report will be provided typically within 30 days of MS analysis.

Sample reception hours: Monday to Friday, 10am-12pm and 2pm-5pm.

When the results of services provided by the UniMS are subjected to publication, an acknowledgement/reference must be added in the adequate section: “MS data provided/obtained by the UniMS – Mass Spectrometry Unit, ITQB/iBET, Oeiras, Portugal”.

UniMS Direction – unims.direction@itqb.unl.pt 

UniMS Technicians – unims.technicians@itqb.unl.pt