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Proteomics Core Facility IIGB

Institute for Integrative Genome Biology

About Proteomics

The core aims to accommodate the research needs of the academic community and provides services, facilities, and expertise to any group seeking to explore proteomics.

We provide a wide array of services for the characterization of protein samples, ranging from discovery proteomics, quantitative Tandem Mass Tag analyses, gel band identification, post-translational modification analyses, co-immunoprecipitation analyses, and more. We also provide sample preparation and data analysis as part of our service.

Samples are processed and analyzed on a sensitive nanoflow liquid chromatography system coupled to a high-resolution Orbitrap Fusion mass spectrometer.

 

Equipment

The proteomics core is equipped with a Thermo Orbitrap Fusion Tribrid ETD mass spectrometer and Thermo Easy nanoLC 1200 liquid chromatography system. This setup allows sensitive and versatile high-resolution data acquisition.

The core also has a variety of equipment specifically for sample preparation and processing, including speed vacuum concentrators, a Precellys tissue/cell homogenizer, and centrifuges.

Data processing is performed on workstations using Proteome Discoverer.

Some peripheral equipment is available for use at an hourly rate by users, see the pricing page.

Instrumentation funding has been supported by NIH grant S10 OD010669

 

  • The Orbitrap Fusion Tribrid Mass Spectrometer (Thermo Fisher Scientific) is a high-resolution, high-sensitivity proteomics platform that integrates three mass analyzers—quadrupole, ion trap, and Orbitrap—and supports HCD, CID, and ETD fragmentation for flexible protein identification, quantification, and structural characterization. Its ETD capability is especially powerful for confidently localizing labile and highly charged post-translational modifications such as phosphorylation, ubiquitination, and SUMOylation, while also enabling global shotgun proteomics, TMT/TMTpro and label-free quantification, and protein–protein interaction studies. With fast scan speeds, high mass accuracy, and robust performance, it serves as a cornerstone instrument for delivering reproducible, scalable data across both routine protein ID and advanced PTM-focused workflows. Liquid Chromatography-Mass Sepctrometry (LC-MS)

  • The Vanquish™ UHPLC–TSQ Quantis™ Plus system (Thermo Fisher Scientific) is a high-sensitivity, high-robustness triple quadrupole LC–MS/MS platform that pairs ultra-high-pressure liquid chromatography with a fast, precise triple quadrupole analyzer to deliver exceptional sensitivity, selectivity, and reproducibility for targeted quantitative analysis. The Vanquish UHPLC provides stable, low-dead-volume separations while the TSQ Quantis Plus enables high-performance multiple reaction monitoring (MRM) for confident quantification across complex biological matrices, making it well suited for routine, high-throughput workflows in a shared core environment. Within a core facility, it serves as a gold-standard platform for targeted proteomics, metabolomics, and small-molecule quantification. Liquid Chromatography-Mass Sepctrometry (LC-MS)

  • The Agilent 1260 Infinity II UHPLC system (Agilent Technologies) is a robust, flexible liquid chromatography platform built for reproducible, high-performance separations across both routine analyses and advanced research, with a modular configuration that supports high-pressure UHPLC operation, precise solvent delivery, and excellent retention time stability for complex biological, chemical, and pharmaceutical samples. Its compatibility with a wide range of columns and mobile phases allows seamless method development and transfer across diverse applications. Within a core facility, it serves as a dependable front-end separation system for mass spectrometry–based workflows as well as standalone LC analyses, ensuring consistent chromatographic performance across user projects. Liquid Chromatography

  • The ECLASSICAL 3200 Series UHPLC/HPLC system is a fully modular liquid chromatography platform that integrates independent modules for solvent delivery (P3200 high-pressure binary pump), autosampling (S3200), column temperature control (T3200 oven), optical detection (D3200 UV/Vis detector), and system control (O3200), providing flexible configuration for a wide range of analytical workflows. Built for stability and reproducibility, it delivers accurate flow control, consistent retention times, and dependable long-term performance, while its modular design allows easy maintenance and method customization for both routine analysis and method development. Within a shared core facility, it can serve as a standalone analytical LC platform or as a front-end separation system for downstream detection, supporting diverse research needs across chemistry, biology, and pharmaceutical sciences.  Liquid Chromatography

  • The Optima™ XPN-80 Ultracentrifuge (Beckman Coulter) is a high-performance preparative ultracentrifugation system capable of extremely high centrifugal forces, designed for high-speed separation of macromolecules, subcellular components, and nanoparticles across biochemical, molecular biology, and biophysical applications. It accommodates multiple rotor types and tube formats for flexible experimental design—including density gradient centrifugation, differential centrifugation, and particle isolation—while advanced control and monitoring features ensure precise speed regulation, temperature stability, and reproducible performance. Within a core facility, it provides a reliable, scalable solution for complex sample preparation and fractionation, supporting both routine workflows and advanced method development. Sample Fractionation

  • The GELFREE® 8100 Fractionation System (Protein Discovery) is a gel-based, solution-phase protein fractionation platform that separates intact proteins by molecular weight while keeping them in liquid form, enabling direct recovery of fractions for downstream analysis rather than relying on traditional slab gels. By combining SDS-PAGE–style size separation with automated fraction collection, it produces highly reproducible, molecular-weight–resolved fractions that are immediately compatible with enzymatic digestion and LC–MS/MS workflows, making it especially powerful for reducing sample complexity prior to deep proteomic analysis. Within a core facility, it supports top-down, middle-down, and enhanced bottom-up proteomics, offering users an additional dimension of separation beyond conventional peptide-level fractionation. Sample Fractionation

  • The Ettan IPGphor IEF System (Cytiva, formerly GE Healthcare Life Sciences) is a high-performance isoelectric focusing platform that uses immobilized pH gradient (IPG) strips to separate proteins by their isoelectric point (pI), serving as the gold-standard first dimension in two-dimensional gel electrophoresis (2D-PAGE) workflows. It provides accurate control of voltage, current, and focusing time for high reproducibility and excellent resolution across a wide range of pH gradients, with flexible programming that optimizes performance for sample types ranging from simple protein mixtures to highly complex biological extracts. Within a core facility, it supports protein-level separation prior to SDS-PAGE or mass spectrometry, offering an orthogonal separation strategy that complements LC–MS–based proteomics. Sample Fractionation

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