Metabolomics Unit

The goal of the Metabolomics Unit is to support researchers in all the steps involved in targeted and non-targeted metabolomics studies. We assist researchers in the experimental design of the study, sample treatment, sample acquisition and data analysis.

Equipment and services

The unit provides the following services:

  • Design and planning metabolomics studies.
  • Metabolite extraction from any type of biological sample.
  • Sample acquisition using LC-MS in an external institute (i.e. UniMS at iBET). 
  • Raw data processing using XCMS and MZmine.
  • Statistical analysis using R, SIMCA and SPSS.
  • Metabolite identification from MS/MS data using metabolomics libraries.

How to use

The service is accessible to iNOVA4Health projects upon consultation. Other projects may be considered, though priority will be given to iNOVA4Health projects. 

  • Costs. LC-MS acquisition fees will be defined with our collaborator partners and covered by the project PI. Additional costs will be applied for non-iNOVA4Health research projects.
  • Consultation:
    • Each project will be pre-assessed based on an initial meeting with Judit Morello for feasibility and assurances of financial responsibility.
    • Groups requesting the service must provide a short statement outlining how the project aligns with the iNOVA4Health project.
    • All requests for new metabolomics projects are discussed between Judit Morello, Paulo Pereira (iNOVA4Health coordinator @NMS) and Sofia Pereira (Metabolomics Unit Scientific Coordinator) prior to confirming acceptance.
    • After acceptance, a proposal with specific outcomes, budget and timeline will be prepared.

Contact Judit Morello,, providing as much detail as possible of your study and anticipated support needs.




Monday to Friday

Phone: 218803000 

Bank transfer

CEDOC- Center for the Study of Chronic Diseases
Rua Câmara Pestana nº 6, 6-A
CEDOC II Building
1150-082 Lisbon


Step 1. First contact. Send an email to copying to Catarina Sequeira, providing as much detail as possible of your study and anticipated support needs.

Step 2. Implement strategies. We will schedule a video conference to discuss your project at length, understand your goals and decide which type of service suits you.

Step 3. Proposal. We will elaborate a proposal with specific outcomes, budget and timeline. Putative outcomes: data pre-processing, statistical analysis, metabolite identification, metabolite quantification, detailed methods writing, detailed results writing with figures. The proposal needs information on how samples were treated and acquired to anticipate problems related with poor data quality.

Step 4. Agreement. An agreement will be signed based on the terms listed below.


  1. You pay 25% of the service upfront[1]. You pay the remaining 75% when the service is completed, and you receive the defined outcomes and a report.
  2. If we fail to deliver the defined outcomes at the agreed timeline, we are obliged to show you that the planned tasks were performed and that different strategies were tried to surmount the encountered problems. Reimbursements of the 25% will be performed only in case of non-compliance.
  3. You must include a reference to our services in the materials and methods of your manuscript(s).


[1] The budget calculation will be made based on the number of hours worked and assuming an hourly value of the PhD researchers of € 27.5 / hour. This hourly rate corresponds to € 21.72 / hour of salary plus 20% of overheads for NMS and 6.6% of revenue for the service. Typically, a standard non-targeted and targeted job lasts for 26 and 10 days respectively.


Sofia de Azeredo Pereira


Judit Morello