Instrumentation

• The Orbitrap Exploris™ 480 mass spectrometer enables highly sensitive and accurate protein identification in complex mixtures. It is well suited for in-depth global analyses using both Data Depended Acquisition (DDA) and Data Independent Acquisition (DIA) methods, and supports targeted quantification via Parallel Reaction Monitoring (PRM). The facility houses three of these instruments.

• The Orbitrap Eclipse™ Tribrid™ mass spectrometer enables highly sensitive and accurate protein identification in complex mixtures. It supports Electron Transfer Dissociation (ETD), allowing detailed analysis of labile post-translational modifications (PTMs) such as phosphorylation and glycosylation. The instrument is compatible with PRM for targeted quantification and is the platform of choice for Tandem Mass Tag (TMT ) experiments using MS3-based methods.

• The Q Exactive™ Orbitrap mass spectrometer is well suited for protein identification and quantification in relatively simple samples, including gel bands, purified proteins, and immunoprecipitates. It also supports targeted quantification using PRM.

• The Vanquish™ Neo system, equipped with a µPAC trap column and a 50 cm µPAC Neo HPLC column, is typically operated in conjunction with the Orbitrap Exploris™ 480 or Orbitrap Eclipse™ Tribrid™ platforms. Standard methods of 38 or 58 minutes enable throughput of approximately 40 or 20 samples per day (SPD), respectively. Gradient conditions can be customized, for example, to support targeted assays.
  
  
• The Evosep™ One system, equipped with a 15 cm Aurora Elite C18 column, requires samples to be loaded onto Evotips prior to analysis. It is most commonly operated in conjunction with the Orbitrap Eclipse™ Tribrid™ platform for TMT experiments, but can also be paired with the Orbitrap Exploris™ 480. Standard gradients of 31 or 58 minutes enable throughput of approximately 40 or 20 SPD, respectively. While gradient customization is not supported, higher-throughput options are available using shorter gradients (80 or 120 SPD) with shorter columns.
  
  
• The EASY-nLC™ 1200 system, equipped with an Acclaim PepMap 100 (2 cm) C18 precolumn and a PepMap RSLC C18 (15 cm) analytical column, is most commonly operated in conjunction with the Q Exactive™ Orbitrap, but can also be paired with other mass spectrometers. A standard 70-minute gradient enables a throughput of approximately 16 SPD. Gradient conditions can be customized, for example, to support targeted assays.

Laser microdissection

• Leica LMD6 enables isolation of specific cells or tissue regions for proteomics analysis, allowing protein profiles to be mapped to their spatial origin and supporting spatial proteomics applications.

Protein extraction

• Bioruptor® Pico for ultrasonication of samples during sample lysis or resuspension.
• QIAGEN TissueLyser II for mechanical lysis and homogenization of samples via bead-beating.
• Barocycler 2320EXT for protein extraction and homogenization using cycles of hydrostatic pressure between ambient and ultra-high levels.
• Precellys Evolution Touch for bead-based mechanical lysis and homogenization of samples via bed-beating with optional cooling.

High-pH fractionation

• Dionex UltiMate 3000 system for high-pH fractionation, primarily used in TMT-labeled workflows.

Pipetting robots

• Opentrons Flex™ for automated sample preparation, with established protocols for SP3 digestion, plasma depletion by MagNet protocol, and phosphopeptide enrichment.
• Opentrons OT-2 for automated liquid pipetting.

Concentration measurements

• DeNovix DS-11 FX+ for NanoDrop measurement of peptide concentrations.
• EPOCH2 Microplate Reader for measurement of protein concentations using BCA assays.

• Secure local servers for proteomics data storage, management, and centralized project organization.
• Controlled access to ensure data integrity and compliance.
• High-performance computing (HPC) recourses for large-scare data processing and computationally intensive workflows (e.g., de novo sequencing).
• Parallel processing capabilities to enhance throughput and efficiency.
• GDPR-compliant data processing and storage, with integration of Computerome resources. (coming soon...)

• Xcalibur™ for instrument control and LC-MS data acquisition.
• Proteome Discoverer™ for processing and quantitative analysis of DDA LC-MS data, integrating database search engines such a Sequence and Mascot, for protein identification.
• Spectronaut® for protein identification and quantitative analysis of DIA LC-MS data via library-based or library-free workflows.
• PEAKS for de novo sequencing and database-assisted analysis of DDA LC-MS data.
• InstaNovo for high-throughput, deep learning-based de novo peptide sequencing of DDA LC-MS data.
• Skyline for data analysis and method development in targeted proteomics (PRM).

• Data analysis, visualization, and statistical inference using R and Python.
• Standardized and reproducible workflows and script-based analysis.
• Custom pipeline development for advanced proteomics applications.