Portuguese Mass Spectrometry Network | - CCMAR -

Portuguese Mass Spectrometry Network

The Portuguese Mass Spectrometry Network (RNEM) is a national infrastructure that provides state-of-art scientific expertise, advanced technology, training and services in the area of mass spectrometry and proteomics.

Included in the Portuguese Roadmap of Scientific Research Infrastructures of Strategic Interest, RNEM currently comprises 14 nodes, including CCMAR, that offers differentiated services, interdisciplinary and aimed at problem-solving. 


Mass Spectrometry    
The Mass Spectrometry at CCMAR is mainly dedicated to Marine Sciences and provides support, training and services in mass spectrometry, particularly in the areas of metabolomics, natural products and marine toxins and contaminants. 


MS Equipment

Orbitrap Elite, ITMS & FTMS, CID MSn, n up to 10, and HCD, with accuracy < 5 ppm under full scan and fragmentation. ESI and APCI sources available.


The MS equipment comprises: 

  • Infusion and UHPLC (Thermo Scientific ultimate 3000) interfaces
  • m/z range: 15 – 4000, Linear trap (ITMS)
  • m/z range: 50 – 4000, Orbitrap (FTMS)
  • Collision Induced Dissociation (CID) MSn, n up to 10
  • Higher energy C-trap Dissociation (HCD)
  • Resolution: up to 240 000 (@m/z 400)
  • Accuracy: < 5 ppm under full scan and MSn



  • Metabolomics
  • Natural products
  • Environmental analysis
  • Food analysis    


GC-MS (Bruker)

The equipment can be used for the analysis of volatile and semi-volatile compounds.


LC Equipment

UHPLC. Thermo Scientific Ultra-Performance Liquid Chromatograph, model Ultimate 3000. DAD and Fluorescence detectors.


Preparative/analytic LC. Shimadzu. Equipped with binary pump, autosampler, fraction collector, DAD and ELSD detectors.



  • Metabolomics (untargeted)
  • LC-MS. Data dependent acquisition with RP-18 and/or HILIC chromatography.
  • Data processing. Compound Discoverer 3.3, metabolomics workflows with statistics and ID using local and online databases such as mzCloud, HMDB and BioCyc. 
  • Analysis of marine biotoxins:
    • DSP toxins: okadaic acid (AO), dynophysistoxins (DTX-1 and DTX-2), yessotoxins (YTX, YTX-OH, h-YTX, h-YTX-OH)
    • AZP toxins: azaspiracid-1 (AZA-1), azaspiracid-2 (AZA-2), azaspiracid-3 (AZA-3)
    • PSP toxins: carbamate saxitoxins (STX, neoSTX), decarbamoylsaxitoxins (dcSTX, dcneoSTX, dc-GTX-2 and dc-GTX-3), gonyautoxins (GTX-1, GTX-2, GTX-3 and GTX-4), N-sulfo-carbamoyl saxitoxins (C1, C2, C3, C4, GTX5 and GTX6)
    • ASP toxins: domoic acid (DA and epi-DA)
    • Other toxins: pectenotoxins (PTX-1 and PTX-2)


Booking | Scheduling: Central de Serviços CCMAR – ccmarcts@ualg.pt
Node coordinatorJosé Paulo da Silva