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U30-S09. Data analysis of proteomics experiments

Data analysis of proteomics experiments

Use of dedicated software for the analysis and interpretation of the results obtained from the proteomic analyses. It includes search engines (MaxQuant, DIANN) 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.

Customer benefits

This service provides comprehensive reports of the data obtained in the proteomic analyses, following the customer’s indications and the objective of each specific project. Upon request, data and reports can be uploaded to private or public repositories.

Target customer

Organizations and research groups focused in biomarker discovery, metaproteomics studies, analysis of specific post-translational modifications, 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

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.

Customer benefits

This service provides quantitative data of proteins and small protein panels, including cytokines, chemokines or specific biomarker candidates, in biological samples. The assays are run with high sensitivity and throughput.

Target customer

Organizations and research groups that aim to quantify in an absolute way single proteins or small panels in large number of samples. Groups interested in cytokine or chemokine profiling.

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

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.

Customer benefits

This service allows the fractionation of complex protein samples prior to proteomic analysis, performing gel-based quantitative proteomic studies by DIGE (differential in-gel electrophoresis), and evaluating protein profiles by SDS-PAGE followed by gel staining.

Target customer

Organizations and research groups interested in protein or proteomic analysis of biological samples.

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

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.

Customer benefits

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

Target customer

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 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

Relative or absolute quantification of individual proteins or protein panels by the analysis of their peptides together with stable isotope labelled (SIL) standards.

Customer benefits

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. The use of isotope labelled standards allows the absolute quantification of the protein/s of interest.

Target customer

Organizations and research groups interested in the analysis and quantification of a protein or panel of proteins with high specificity.

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

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. Quantifications can be performed via label-free (LFQ) or protein/peptide isotopic labelling using SILAC, iTRAQ or TMT reagents.

Customer benefits

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.

Target customer

Organizations and research groups interested in 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

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).

Customer benefits

Identification of proteins by mass spectrometry allows the characterization of biological samples, analysis of protein interactions (e.g. pull-down assays), peptide sequencing, etc. Identifications are performed with the highest specificity.

Target customer

Organizations and research groups interested in small or large-scale protein analysis.

Additional information

E03 MALDI-TOF/TOF System

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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

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.

Customer benefits

This service is useful to characterize a variety of biomolecules by the determination of their molecular mass with an extreme high precision. This is an essential step in many biotechnological strategies involving protein synthesis and production.

Target customer

Organizations or research groups aiming to characterize specific proteins, peptides or other biomolecules by the determination of their molecular mass.

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

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.

Customer benefits

Biological samples are processed and prepared following standardized protocols by personnel highly specialized in techniques for protein analysis.
The service allows organizations without prior experience in protein or proteomic analysis to avoid performing any experiment, only needing to provide the biological specimen to the Unit.

Target customer

Organizations or research groups interested in performing protein or proteomic analyses in a wide range of biological samples: cells, tissues, biofluids, protein extracts, etc.

U30 S01 Sample preparation for proteomic analysis
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U30-E05. Small equipment for protein detection/quantification

Small equipment for protein detection/quantification

Description: Under this concept, the Unit has the following instruments:

  1. MagPix reader (Luminex), for the readout of magnetic bead–based immunoassays designed on xMAP beads. Allows the quantification of up to 50 analytes per sample.
  2. DIGE Imager (GE), for the digitalization of difference in-gel electrophoresis (DIGE) gels or stained with fluorescence (SYPRO, etc.).
  3. Amersham Imager 600 (GE), for the detection and digitalization of fluorescence or quimioluminiscence signals in gels or membranes.

Applications: Detection and/or quantification of proteins.

E05 MagPix reader
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