U30. Proteomics - Services

U30-S09. Data analysis of proteomics experiments

Data analysis of proteomics experiments

Description: Use of dedicated software for the analysis and interpretation of the results obtained from the proteomic analyses. It includes search engines (MaxQuant, MSFragger) for protein identification and quantification, software for statistical analysis (Perseus) and programs for integrated solutions (Peaks) that also enable the analysis of post-translational modifications (PTMs), sequence variants and mutations.

Applications: Biomarker discovery, proteomic profiling, metaproteomics studies, PTM analysis, etc.

U30 S09 Data analysis of proteomics experiments

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U30-S08. Luminex or ELISA assay development and analysis

Luminex or ELISA assay development and analysis

Description: Design and development of immunoassays employing antibody pairs for the detection and absolute quantification of target proteins. These can be set up on a traditional ELISA format, or coupled to magnetic beads (xMAP, Luminex) for multiplex detection. Optimization procedures, including cross-reactivity assays, are performed to standardize the assay protocol. Alternatively, this service may also use commercial ELISA or multiplex kits for the analysis of specific protein panels.

Applications: Quantification of proteins and protein panels, including cytokines, chemokines or specific biomarker candidates, in biological samples.

U30-S08 : Luminex or ELISA assay development and analysis

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U30-S07. Protein separation by one- or two-dimensional gel electrophoresis

Protein separation by one- or two-dimensional gel electrophoresis

Description: Separation of complex protein mixtures on isoelectric focusing strips (according to their charge) and/or SDS-PAGE gels (according to their size), as a step for further protein or proteomic analysis.

Applications: Fractionation of complex protein samples prior to proteomic analysis, gel-based quantitative proteomic studies by DIGE (differential in-gel electrophoresis), evaluation of protein profiles.

U30-S07 Protein separation by one- or two-dimensional gel electrophoresis

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U30-S06. Protein or peptide separation by liquid chromatography

Protein or peptide separation by liquid chromatography

Description: Separation of complex protein or peptide mixtures using chromatography columns. The chromatographic services offered by the Unit include strong cation exchange (IEX), reversed phase (C18), gel filtration and immunoaffinity for the removal of the top 14 most abundant proteins in human plasma.

Applications: Fractionation of complex protein or peptide samples prior to proteomic analysis, preparation of serum, plasma and other biofluids for shotgun proteomics through the depletion of their most abundant proteins.

U30 S06 Protein or peptide separation by liquid chromatography

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U30-S05. Targeted proteomics analysis by MRM or PRM-MS

Targeted proteomics analysis by MRM or PRM-MS

Description: Relative or absolute quantification of protein panels by the monitorization of their peptides together with stable isotope labelled (SIL) standards.

Applications: This strategy is employed to verify or validate biological hypotheses with the highest specificity, as it detects the protein sequence and is not dependent on antibodies.

U30-S05 Targeted proteomics analysis by MRM or PRM-MS

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U30-S04. Quantitative shotgun proteomics by nLC-MS/MS

Quantitative shotgun proteomics by nLC-MS/MS

Description: Large-scale relative quantification of proteins in biological samples by nano-flow high performance liquid chromatography combined with mass spectrometry. It can use either data-dependent (DDA) or data-independent (DIA) acquisition modes. Quantification can be performed via label-free (LFQ) or protein/peptide isotopic labelling using SILAC, iTRAQ or TMT reagents. The output of this analyses are lists of proteins identified in the samples together with quantitative information obtained from the area displayed by each peptide in the mass spectra, and can then be compared across experimental conditions.

Applications: Protein profiling, biomarker discovery, drug discovery (protein target identification), development of precision medicine approaches, etc.

U30-S04 Quantitative shotgun proteomics by nLC-MS/MS

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U30-S03. Protein identification by mass spectrometry (MS) or MS/MS

Protein identification by mass spectrometry (MS) or MS/MS

Description: Identification of proteins in biological samples, either by intact protein analysis (MALDI-TOF) or protein digestion followed by peptide mass fingerprinting (PMF, MS) or peptide fragmentation (MS/MS).

Applications: Protein analysis, characterization of biological samples, analysis of protein interactions (e.g. pull-down assays).

U30 S03 Protein identification by mass spectrometry (MS) or MS/MS

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U30-S02. Determination of molecular mass of peptides, proteins and other biomolecules

Determination of molecular mass of peptides, proteins and other biomolecules.

Description: Analysis of intact proteins, peptides and other biomolecules such as oligonucleotides using mass spectrometry (MALDI-TOF or ESI-Q-TOF) for the determination of their exact molecular mass.

Applications: Characterization of biomolecules.

U30 S02 Determination of molecular mass of peptides, proteins and other biomolecules

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U30-S01. Sample preparation for proteomic analysis

Sample preparation for proteomic analysis

Description: This service includes all necessary steps to prepare samples for different proteomic analyses: protein extraction from tissues, cells or fluids, precipitation, cleaning, desalting, quantification and digestion (in gel or in solution) with proteolytic enzimes (trypsin, chymotrypsin, lys-C…), to obtain the correspondent peptides.

Applications: All experiments involving proteins.

U30 S01 Sample preparation for proteomic analysis

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U30. Proteomics - Services

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