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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-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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U30-E04. Small equipment for protein separation

Small equipment for protein separation

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

  1. High-performance liquid chromatography (HPLC) system with UV detector (Agilent 1200 Series), for the chromatographic separation of proteins by reversed phase, ion exange, gel filtration or affinity.
  2. Two IPGPhor systems (GE Healthcare), for the separation of proteins by isoelectric focusing.
  3. Protein electrophoresis units: MiniProtean (Bio-Rad), SE600 Ruby (GE Healthcare) y Ettan™ DALTsix (GE Healthcare), for running gels up to 24×26 cm to separate proteins according to their size.
  4. Microfraction collector and spotter SunCollect (SunChrom), to collect fractions coming out of the nLC and deposit themo onto MALDI plates for mass spectrometry. 

Applications: Separation of proteins in liquid or gel supports, according to a wide variety of physicochemical properties.

E04 SunChrom spotter
E04 HPLC 1200 series
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U30-E03. MALDI-TOF/TOF System

MALDI-TOF/TOF System

Description: 4800 Proteomics Analyzer (Sciex)

Technical specifications: Mass spectrometer equipped with a matrix-assisted laser desorption/ionization (MALDI) source, using a Nd:YAG 200-Hz laser, and two time-of-flight mass analyzers in tandem with a high-energy collision-induced disociation (CID) chamber for ion fragmentation. It has a variable ion path length to accomodate MS linear, MS reflector and MS/MS acquisition modes.

Applications: Determination of molecular masses of peptides, proteins and other biomolecules. Protein identification by peptide fingerprint or peptide fragmentation. Shotgun quantitative proteomics analyses by isotopic labeling and LC-MALDI workflows.

E03 MALDI-TOF/TOF System
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U30-E02. QTRAP LC-MS/MS System

QTRAP LC-MS/MS System

Description: Tempo™ nanoLC-2D liquid chromatography system coupled to QTRAP5500 mass spectrometer (Sciex).

Technical specifications: The QTRAP® 5500 LC-MS/MS system (Sciex) is a triple quadrupole combined with a trap-type accelerator. It has two electrospray ionization sources (nano source and turbo source).

Applications: Determination of molecular masses of peptides, proteins and other biomolecules. Absolute quantification of proteins using isotope-labeled standards. Targeted quantitative proteomics analyses by multiple reaction monitoring (MRM).

U30 E02 QTRAP LC-MS/MS System
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