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TripleTOF combined with SelexION™ Technology
SCIEX, model 6600

The new SCIEX TripleTOF 6600 system is the top performing TripleTOF in the market. It is a high performance system with enhanced reproducibility 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. Comprehensive qualitative extrapolation is possible with MS/MS acquisition and with a single injection. The complete digital archive obtained from the single injection can be interrogated multiple times (data independent algorithm). 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”.

This system can be coupled to a LC with micro or nano flow, depending on the application. Additionally, it can be coupled to the new Capillary Electrophoresis instrument (CESI 8000 Plus), which enables nano sample injection and has particular use for differentially charged molecules, such as in PTM peptides.



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 specially 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.



SCIEX, model 8000 Plus 

The CESI 8000 Plus system 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, thanks to the nanovial and a positive pressure system. Alternatively, a specific set of charged molecules can be injected through electrokinetic injection.

CE can be applied to different fields, such as Biologics analysis, Proteomics, Metabolomics and Analytical Chemistry. 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.



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). 

For analysis in the MALDI-TOF/TOF, the samples are co-crystallized with an organic matrix and then ionized by the action of a laser. After ionization the charged particles of the analyte fly through the TOF and the mass-to-charge ratio of the different components is determined.

Sample analysis can be performed using linear mode for analytes with molecular weights above the 4000 Da or in reflector MS mode for analytes below the 4000 Da. Samples previously analyzed in reflector MS mode can be further analyzed by MSMS mode in order to obtain a fragmentation pattern.

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.

The system is easily operated and therefore the UniMS may provide training for independent users if the workload justifies.


Q Exactive™ Hybrid Quadrupole-Orbitrap™ Mass Spectrometer

ThermoFisher, model Focus

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, allowing a wide linear dynamic range and confident identification and confirmation. The fast polarity switching enables processing of more classes of compounds in a single analysis. The high scan speed (up to 12 Hz) assures compatibility with fast chromatography and high-throughput screening.

The hybrid quadrupole-Orbitrap 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 for ultimate scan speed and quantitative performance

  • Variable data-independent acquisition (vDIA) for qualitative coverage of unknowns without compromising quantitative performance

  • Selected-ion monitoring (SIM) for simple setup and highest sensitivity

  • Parallel-reaction monitoring (PRM) for high selectivity and high throughput with confident confirmation

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.



This is an ion trap mass analyzer, coupled to an HPLC, THERMOFINIGAN model SURVEYOR. This ion trap MS can be used for sample direct infusion or coupled (on-line) to an HPLC system (Surveyor, Thermofinnigan) 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.


BRUKER, model ESQUIRE 3000+

This is a direct infusion ion-trap that can be coupled to soft (electrospray ionization - ESI or nano ESI) or chemical (APCI, Atmospheric Pressure Chemical Ionization) ionization sources. This equipment is used mostly for characterization of biomolecules and small molecules synthesised by ITQB/iBET research groups.






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