Mass Spectrometry Laboratory

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About the facility

The Mass Spectrometry Laboratory (MAS) allows users to conduct experiments that use proteomics based on mass spectrometry. MAS offers technical and scientific support at all project stages, including experimentation: design, sample preparation, sample analysis using liquid tomography tandem mass spectrometry, and data analysis.

How to submit research proposals

To use MAS you must submit a proposal to SAU Online. If you have questions, e-mail the CNPEM User Office at edu@cnpem.br. Each year, proposals are submitted in August for projects to be carried out during the following year.

PREPARE YOUR SAMPLE

SUBMIT YOUR PROPOSAL

Equipment

  • EASY-nLC II acoplado ao LTQ Orbitrap Velos ETD, Thermo Scientific
    • Funded via FAPESP/EMU project 2009/54067-3, acquired in 2011. This system integrates a high-resolution Orbitrap mass analyzer with the sensitivity and speed of the linear ion trap (LTQ), allowing highly sensitive experiments with sub-ppm resolution. The equipment makes it possible to apply multiple techniques involving fragmentation, collision-induced dissociation (CID), higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD), and has been dedicated to sample quality control and identification and quantification of proteins in complex samples.
  • LC Evosep One acoplado ao Orbitrap Exploris 240, Thermo Scientific
    • Evosep: funded via MS/CNPq project Saúde de Precisão, acquired in 2024; Exploris 240: funded via MCTI project Iniciativa de Combate a Viroses Emergentes, acquired in 2021. This system combines the robust and reproducible nature of the LC Evosep One, which focuses on high productivity and low variability between injections, with the Orbitrap Exploris 240 mass spectrometer, which offers high resolution, precision measurement of mass (<1 ppm), and versatility in data acquisition (DDA, DIA, PRM). This platform enables the scalability of proteomic analyses, maintaining sensitivity and reliability even in projects with high analytical demands;
  • Vanquish Neo UHPLC acoplado ao Orbitrap Astral, Thermo Scientific
    • Funded via FAPESP/EMU project 22/11476-5, acquired in 2024. The Orbitrap Astral is the newest generation of high-resolution mass spectrometer, and combines three modules: high-resolution quadrupole, the Orbitrap analyzer and the new Astral analyzer. This hybrid architecture allows ultra-fast data acquisition, with high proteome coverage, femtomolar sensitivity and robust quantification even in limited samples. Coupled with the Vanquish Neo UHPLC system (which is optimized for nanoflow and low volume), it is ideal for applications such as single-cell proteomics, analysis of clinical biopsies and identification of post-translational modifications in complex samples
  • CellenONE X1, Scienion
    • Funded via FAPESP/EMU project 22/11476-5, acquired in 2024. State-of-the-art microdispensing equipment that combines image-based capture with ultra-smooth acoustic dispensing, permitting precise isolation of individual cells and subcellular particles. It is the central tool for single-cell proteomics workflows, guaranteeing cell integrity and reproducibility for subsequent analyses.

Main competencies and techniques

  • Large-scale proteomics and peptidomics: Identification and quantification of proteins and peptides in complex samples, with or without isotopic labeling (label-free, TMT, SILAC, etc.)
  • Spatial proteomics: Analysis of proteins with preserved spatial resolution, using laser microdissection combined with proteomics
  • Analysis of post-translational modifications (PTMs): Mapping and quantification of modifications including phosphorylation, glycosylation, ubiquitination and acetylation
  • Structural proteomics: Detection of protein-protein interactions, conformations and cross-linking
  • Single-cell proteomics: Quantification of the proteome in individual isolated cells, coupled to the CellenONE system
  • Computational proteomics: Processing, statistical analysis and biological interpretation of omics data, using tools such as Mascot, Peaks, MaxQuant, Spectronaut, DIA-NN, Proteome Discoverer, FragPipe, Perseus, Skyline and customized bioinformatics platforms

meet our team

Adriana Franco Paes Leme

Coordinator

mas@lnbio.cnpem.br

Bianca Alves Pauletti

Specialist

Romenia Ramos Domingues

Specialist

Sami Yokoo

Specialist