i3S Proteomics platform provides access to mass spectrometry analysis of protein samples from extracts, solutions and gel bands. Our major instrumentation includes a Ultra-high resolution Tribrid Orbitrap Eclipse with ion mobility interface and a Orbitrap Q-Exactive  (Thermo Scientific).  Both mass spectrometers are equipped with a dedicated nano-LC system, Vanquish neo and Ultimate 3000, respectively. Sample ionization is performed by 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)

• Molecular weight determination of biomolecules including peptides, proteins or metabolites;
• Protein identification of clinical (fresh, frozen or FFPE) and 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…).

Equipment:

• Tribrid Orbitrap mass spectrometer (Eclipse, Thermo Scientific)
• Differential Ion Mobility Interface - FAIMS Pro (Thermo Scientific)
• 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)
• GS900 densitometer (Bio-rad)
• Odyssey CLx Imaging System (Li-Cor)

Software:

• Proteome Discoverer v3.0 (Thermo Scientific)
• Mascot v2.6 (Matrix Science)

Proteomics Scientific Platform selected key publications:

1. Osório H, Silva C, Ferreira M, Gullo I, Máximo V, Barros R, Mendonça F, Oliveira C, Carneiro F (2021) Proteomics Analysis of Gastric Cancer Patients with Diabetes Mellitus. J Clin Med 10, 407. doi.org/10.3390/jcm10030407

2. Poças J, Marques C, Gomes C, Otake AH, Pinto F, Ferreira M, Silva T, Faria-Ramos I, Matos R, Ribeiro AR, Senra E, Cavadas B, Batista S, Maia J, Macedo JA, Lima L, Afonso LP, Ferreira JA, Santos LL, Polónia A, Osório H, Belting M, Reis CA, Costa-Silva B, Magalhães A (2023) Syndecan-4 is a maestro of gastric cancer cell invasion and communication that underscores poor survival. Proceedings of the National Academy of Sciences of the United States of America 120. doi.org/10.1073/pnas.2214853120

3. Martins ÁM, Lopes TM, Diniz F, Pires J, Osório H, Pinto F, Freitas D, Reis CA (2023) Differential Protein and Glycan Packaging into Extracellular Vesicles in Response to 3D Gastric Cancer Cellular Organization. Advanced Science 10.  doi.org/10.1002/advs.202300588

4. Ruivo CF, Bastos N, Adem B, Batista I, Duraes C, Melo CA, Castaldo SA, Campos-Laborie F, Moutinho-Ribeiro P, Morão B., Costa-Pinto A, Silva S, Osório H., Ciordia S, Costa JL, Goodrich D, Cavadas B, Pereira L, Kouzarides T, Macedo G, Maio R, Carneiro F, Cravo M. Kalluri R, Machado JC, Melo SA (2022) Extracellular Vesicles from Pancreatic Cancer Stem Cells Lead an Intratumor Communication Network (EVNet) to fuel tumour progression. Gut 71, 2043-2068. doi.org/10.1136/gutjnl-2021-324994

5. Gaiteiro C, Soares J, Relvas-Santos M, Peixoto A, Ferreira D, Paulo P, Brandão A, Fernandes E, Azevedo R, Palmeira C, Freitas R, Miranda A, Osório H, Prieto J, Lima L, Silva AMN, Santos LL, Ferreira JA (2022) Glycoproteogenomics characterizes the CD44 splicing code associated with bladder cancer invasion. Theranostics 12, 3150-3177. doi.org/10.7150/thno.67409

6. Moreira AM, Ferreira RM, Carneiro P, Figueiredo J, Osório H, Barbosa J, Preto J, Pinto-do-Ó P, Carneiro F, Seruca R (2022) Proteomic Identification of a Gastric Tumor ECM Signature Associated With Cancer Progression. Frontiers in Molecular Biosciences 9 doi.org/10.3389/fmolb.2022.818552

7. Marques MS, Costa AC, Osório H, Pinto ML, Relvas S, Dinis-Ribeiro M, Carneiro F, Leite M, Figueiredo C (2021) Helicobacter pylori PqqE is a new virulence factor that cleaves junctional adhesion molecule A and disrupts gastric epithelial integrity. Gut Microbes 13, 1-21. doi.org/10.1080/19490976.2021.1921928

8. Zhang H, Freitas D, Kim HS, Fabijanic K, Li Z, Chen H, Mark MT, Molina H, Martin AB, Bojmar L, Fang J, Rampersaud S, Hoshino A, Matei I, Kenific CM, Nakajima M, Mutvei AP, Sansone P, Buehring W, Wang H, Jimenez JP, Cohen-Gould L, Paknejad N, Brendel M, Manova-Todorova K, Magalhães A, Ferreira JA, Osório H, Silva AM, Massey A, Cubillos-Ruiz JR, Galletti G, Giannakakou P, Cuervo AM, Blenis J, Schwartz R, Brady MS, Peinado H, Bromberg J, Matsui H, Reis CA, Lyden D (2018) Identification of distinct nanoparticles and subsets of extracellular vesicles by asymmetric flow field-flow fractionation. Nat Cell Biol. 20, 332-343. doi.org/10.1038/s41556-018-0040-4

9. Osório H, Reis C (2013) Mass spectrometry methods for studying glycosylation in cancer. Methods in Molecular Biology 1007, 301-316. doi.org/10.1007/978-1-62703-392-3_13

10. Gomes C, Almeida A, Ferreira JA, Silva L, Santos-Sousa H, Pinto-de-Sousa J, Santos LL, Amado F, Schwientek T, Levery S, Mandel U, Clausen H, David L, Reis CA, Osório H (2013) Glycoproteomic analysis of serum from patients with gastric precancerous lesions. J Proteome Res 12, 1454-1466. doi.org/10.1021/pr301112x

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