Proteomics and protein technologies are fundamental tools for molecular biology, biomedicine and translational research, and understanding the changes in protein abundances, protein localization, protein modifications, and protein interactions, are crucial steps toward the elucidation of mechanism of action for health and disease conditions.
The Proteomics Area includes the mass spectrometry-based Proteomics Unit of the Center for Genomic Regulation and University Pompeu Fabra and the Proteomics Facility of the Centre for Omics Sciences (COS) node that offer a common catalogue of services with a unique access portal.
The Proteomics Unit at CRG is a joint unit of the CRG and the University Pompeu Fabra that offers mass spectrometry-based proteomics analyses with strong added value to the scientific community and it is located at the Parc de Recerca Biomèdica de Barcelona (PRBB) building and embedded in the Core Facilities program of the CRG.
The Proteomics Facility of the COS, a joint Unit of University Rovira i Virgili and the Technological Centre Eurecat, is focused on profiling and quantifying proteins of experiments that include chromatographic and electrophoretic systems for protein and peptide separation coupled to the state-of-the-art mass spectrometry systems. Its relevance in the sector lies in the provision of peptidomics, MS-imaging, intact protein analysis, among other common proteomic analysis.
The Proteomics Area of the OmicsTech guides researchers at any proteomics project phase from the design of the experiments to the data analysis.
For further information and discussion of potential collaborations with the PP-CRG or COS nodes, please contact proteomics@omicstech-icts.org
Applications
Characterization of protein interactors of a target protein pulled down by affinity purification, immunoprecipitation or labelling strategies. The expected outcome is a list of proteins that interact with a bait protein using statistical assessment to identify bona fide interactors.
Identification of proteins in a gel band or overexpressed in an expression system of choice. The expected outcome is a list of peptides and proteins identified in the sample of interest.
Quantification of proteins in different conditions relative to a control either without any prior protein labelling or using labelling techniques like SILAC, TMT, etc. Sample types include whole cell extracts, exosomes, secretomes, and liquid biopsies, among others. The expected outcome is a list of quantified proteins relative to control samples, in which each protein is provided with a fold-change and an adjusted p-value.
Quantification of proteins in different conditions relative to a control combining labelling techniques like SILAC, TMT, etc. and sample fractionation. Sample types include whole cell extracts, exosomes, secretomes, and liquid biopsies, among others. The expected outcome is a list of quantified proteins relative to control samples, in which each protein is provided with a fold-change and an adjusted p-value.
Quantification of phosphopeptides in different conditions relative to a control without requiring any prior protein labelling or using labelling techniques like SILAC, TMT, etc. The expected outcome is a list of quantified phosphopeptides relative to control samples, in which each phosphopeptide is provided with a fold-change and an adjusted p-value.
Relative quantification of specific post-translational modifications (PTMs) in purified proteins including phosphorylations, acetylations, methylations or ubiquitylations. The expected outcome is a list of quantified post-translational modified peptides relative to their control samples. Each modified peptide is provided with a fold-change and an adjusted p-value.
Relative quantification of specific post-translational modifications (PTMs) in purified histones. The expected outcome is a list of quantified post-translational modified peptides relative to their control samples. Each modified peptide is provided with a fold-change and an adjusted p-value.
Structural elucidation of purified protein complexes using cleavable chemical crosslinkers and mass spectrometry.
Targeted quantification of a set of proteins of interest in large number of samples. The expected outcome is a list of quantified proteins relative to control samples, in which each protein is provided with a fold-change and an adjusted p-value.
Bioinformatic Applications
Spectra interpretation using commercial and open source software like Proteome Discoverer, MaxQuant, PEAKS, Spectrum Mill, fragpipe, Protein Scape, Skyline and Mascot.
Univariate and multivariate statistical analyses (statistical inference, PCA, clustering, correlations, PLSDA, etc), and pathway enrichment downstream analysis using several software suites like Mass Profiler Professional, Gene Spring, Sieve 1.4, Progenesis, Proteome Discoverer, and FragPipe Analyst, among others.
Bacterial taxonomic identification using MALDI-TOF protein spectra using the Biotyper (Bruker)
Equipment
The Orbitrap Astral Mass Spectrometers combine a quadrupole, an Orbitrap, and the novel Astral mass analyzer to set a new standard in mass spectrometry. They enhance data-independent acquisition (DIA) with unprecedented data quality, faster throughput, and deeper coverage. These instruments are capable of analyzing 180 samples daily and identifying over 8,000 protein groups per sample, and they excel in high dynamic range and precision. These instruments supports single-cell proteomics, providing insights into disease mechanisms by measuring thousands of proteins with high sensitivity and accuracy, crucial for precision medicine and understanding biological complexity.
The Hybrid Orbitrap Mass Spectrometers are (tri-)hybrid high-resolution mass spectrometers that combine quadrupoles, ion traps, and orbitrap mass analysers to offer a great flexibility and a wide range of applications. Orbitrap mass spectrometers deliver excellent mass resolution and mass accuracy in a single compact and easy-to-use instrument. These high-resolution accurate-mass systems detect a wide range of compounds, peptides and small molecules during both targeted and untargeted analyses, without losing selectivity or sensitivity.
The Agilent 6490 Triple Quadrupole mass spectrometer incorporates iFunnel technology to achieve new levels of sensitivity and dynamic range for detection of target compounds in complex matrices. The innovative design of the ion funnel reduces contamination and neutral molecules thus improving overall signal and reducing system noise.
The Agilent 6470 Triple Quadrupole is equipped with an Agilent Jet Stream ion source and a curved geometry collision cell. These innovations enable the reliable detection of target compounds at low levels in diverse matrices, while achieving wide linear dynamic range.
The MALDI (Matrix Assisted Laser Desorption/Ionization) tandem mass spectrometer specially designed for automated MS and MS/MS high throughput identification of samples. Tandem Mass Spectrometry is a technique that utilizes more than one mass selective stage in a mass spectrometer.
The Agilent 6550 Q-TOF incorporates iFunnel technology which increases ion transfer and enables higher sensitivity and lower detection levels. It provides both qualitative and quantitative data with high resolution and accurate mass.
Bravo is Agilent's automated liquid handling platform for processing up to 96 samples.
The cryostat is an instrument that has been designed for rapid freezing and sectioning of tissue samples.
Luminex MAGPIX system is a compact instrument for multiplexed protein quantification based on immunoassays. The system can perform up to 50 different tests in a single reaction volume and reads 96-well-plates in a reduced amount of time. The Luminex MAGPIX system is supported by a broad menu of commercially available assay kits, as well as reagents to build your own assays.
