Where Ideas Grow


i3S Proteomics platform provides access to mass spectrometry analysis of protein samples from extracts, solutions and gel bands. We are equipped with a LC-MS system comprehending a nanoUHPLC on-line coupled to a high-resolution accurate-mass Orbitrap mass spectrometer (Q Exactive, Thermo Scientific) with a nano electrospray ionization source (nanoESI).

 We are available to perform the following studies:

  1. molecular mass determination of biomolecules including metabolites, peptides or proteins.
  2. protein identification by high-resolution accurate mass spectrometry, LC-MS/MS.
  3. high-throughput quantitation of protein expression levels (label-free or labeled quantitation).
  4. targeted protein quantitative analysis.
  5. characterization of protein post-translational modifications including phosphorylation, acetylation, glycosylation, among others.

The Proteomics platform is prepared to work in variety of experimental workflows in order to provide answers to scientific questions and addressing the researchers needs. We offer our scientific and technical expertise with protocol design, experimental execution, results/data interpretation, and consultancy. We are available to provide assistance in grant proposals and project execution. We also provide training in workshops and pre-/post-graduate courses.

In addition, the Proteomics platform is integrated at RNEM, the Portuguese Mass Spectrometry Network. RNEM is included in the FCT's Research Infrastructures Roadmap.

Contacts: proteomics@i3s.up.pt   | Tel:+351 22 040 8821  | Lab 008S3 (Ext. 6053)

Platform Head



  • Molecular weight determination of biomolecules including peptides, proteins or metabolites;
  • Protein identification of biological samples (in solution or in gel);
  • Quantitation of protein expression levels (label free or labeled);
  • Implementation of Data dependent analysis (DDA) or Data independent analysis (DIA) proteomics workflows;
  • Characterization of protein post-translational modifications (e.g. phosphorylation, glycosylation, acetylation, etc…).



  • Hybrid Quadrupole-Orbitrap mass spectrometer (Q-Exactive, Thermo Scientific);
  • nanoUHPLC (Ultimate 3000, Thermo Scientific)
  • nanoESI source (Easy-Spray, Thermo Scientific);
  • SpeedVac sample concentrator (Thermo Scientific);
  • GS800 densitometer (Bio-rad)



  • Proteome Discoverer v2.4 (Thermo Scientific)
  • Mascot v2.6 (Matrix Science)


Proteomics Scientific Platform selected key publications:

Osório H, Silva C, Ferreira M, Gullo I, Máximo V, Barros R, Mendonça F, Oliveira C, Carneiro F., 
Proteomics Analysis of Gastric Cancer Patients with Diabetes Mellitus. J Clin Med10(3):407, 2021.
DOI:  10.3390/jcm10030407

Zhang H., Freitas D., Kim H., Fabijanic K., Li Z., Chen H., Mark M., Molina H., Martin A., Bojmar L., Fang J., Rampersaud S., Hoshino A., Matei I., Kenific C., Nakajima M., Mutvei A., Sansone P., Buehring W., Wang H., Jimenez J., Cohen-Gould L., Paknejad N., Brendel M., Manova-Todorova K., Magalhães A., Ferreira J., Osório H., Silva A., Massey A., Cubillos-Ruiz J., Galletti G., Giannakakou P., Cuervo A., Blenis J., Schwartz R., Brady M., Peinado H., Bromberg J., Matsui H., Reis C., Lyden D.,
Identification of distinct nanoparticles and subsets of extracellular vesicles by asymmetric flow field-flow fractionation. Nature Cell Biology20(3):332-343, 2018.
DOI: 10.1038/s41556-018-0040-4 SCOPUS: 85042193942. .

Korsak B., Almeida G., Rocha S., Pereira C., Mendes N., Osório H., Pereira P., Rodrigues J., Schneider R., Sarmento B., Tomé J., Oliveira C.,
Porphyrin modified trastuzumab improves efficacy of HER2 targeted photodynamic therapy of gastric cancer. International Journal of Cancer141(7):1478-1489, 2017.
DOI: 10.1002/ijc.30844 SCOPUS: 85022335625. .

Osório H., Reis C.,
Mass spectrometry methods for studying glycosylation in cancer. Methods in Molecular Biology1007:301-316, 2013.
DOI: 10.1007/978-1-62703-392-3-13 SCOPUS: 84883156078. .

Catera M., Borelli V., Malagolini N., Chiricolo M., Venturi G., Reis C., Osorio H., Abruzzo P., Capri M., Monti D., Ostan R., Franceschi C., Dall'Olio F.,
Identification of novel plasma glycosylation-associated markers of aging. Oncotarget7(7):7455-7468, 2016.
DOI: 10.18632/oncotarget.7059 SCOPUS: 84958817824. .

Reis C., Osorio H., Silva L., Gomes C., David L.,
Alterations in glycosylation as biomarkers for cancer detection. Journal of Clinical Pathology63(4):322-329, 2010.
DOI: 10.1136/jcp.2009.071035 SCOPUS: 77950410995. .

Almeida M., Mesquita F., Cruz R., Osório H., Custódio R., Brito C., Vingadassalom D., Martins M., Leong J., Holden D., Cabanes D., Sousa S.,
Src-dependent tyrosine phosphorylation of non-muscle myosin heavy chain-IIA restricts Listeria monocytogenes cellular infection. Journal of Biological Chemistry290(13):8383-8395, 2015.
DOI: 10.1074/jbc.M114.591313 SCOPUS: 84925760833. .

Maia L., Magalhães R., Freitas J., Taipa R., Pires M., Osório H., Dias D., Pessegueiro H., Correia M., Coelho T.,
CNS involvement in V30M transthyretin amyloidosis: Clinical, neuropathological and biochemical findings. Journal of Neurology Neurosurgery and Psychiatry86(2):159-167, 2015.
DOI: 10.1136/jnnp-2014-308107 SCOPUS: 84921404034. .

Branquinho R., Sousa C., Lopes J., Pintado M., Peixe L., Osório H.,
Differentiation of Bacillus pumilus and Bacillus safensis Using MALDI-TOF-MS. PLoS ONE9(10):, 2014.
DOI: 10.1371/journal.pone.0110127 SCOPUS: 84907978977. .

Gomes C., Almeida A., Ferreira J., Silva L., Santos-Sousa H., Pinto-De-Sousa J., Santos L., Amado F., Schwientek T., Levery S., Mandel U., Clausen H., David L., Reis C., Osório H.,
Glycoproteomic analysis of serum from patients with gastric precancerous lesions. Journal of Proteome Research12(3):1454-1466, 2013.
DOI: 10.1021/pr301112x SCOPUS: 84874635340. .


The Proteomics platform is integrated at RNEM, the Portuguese Mass Spectrometry Network. RNEM is included in the FCT's Research Infrastructures Roadmap.