Instrumentation

The Thermo Fisher Scientific Orbitrap Ascend Tribrid mass spectrometer is a high-performance hybrid mass spectrometer combining quadrupole, Orbitrap, and ion trap mass analysis with advanced ion-routing capabilities. 

Coupled with FAIMS Pro, the system provides gas-phase ion separation prior to mass analysis, helping reduce chemical background and improve selectivity and proteome coverage for complex samples. Its high sensitivity, fast acquisition speed, and flexible fragmentation capabilities make it well suited for high-throughput and in-depth proteomic analyses.

In its current setup, Orbitrap Ascend is used for data-independent acquisition (DIA), TMT-based quantitative proteomics and phosphoproteomics using MS2 and MultiNotch MS3 (SPS-MS3) workflows, plasma proteomics, and other high-sensitivity proteomic applications. FAIMS-enabled acquisition provides additional gas-phase ion separation for the analysis of complex biological samples.

Note: The Orbitrap Ascend is coupled to a Vanquish Neo UHPLC system and equipped with a nanospray source and FAIMS Pro interface.

The Thermo Fisher Scientific Q Exactive HF is a hybrid quadrupole-Orbitrap mass spectrometer featuring an ultra-high-field Orbitrap analyzer. 

The instrument provides high-resolution, accurate-mass measurements together with fast acquisition and HCD fragmentation, making it well suited for both discovery and targeted proteomic applications.

In its current setup, Q Exactive HF is used for standard qualitative proteomics and protein identification, protein–protein interaction studies, targeted proteomics using parallel reaction monitoring (PRM), and cross-linking mass spectrometry (XL-MS).

Note: The Orbitrap Fusion and Q Exactive HF are each equipped with dedicated RSLCnano (Dionex) UHPLC systems and nanospray sources.

The Seer Proteograph SP200 Automation Instrument is an automated sample preparation platform designed for deep proteomic profiling of complex biological samples, particularly plasma and cerebrospinal fluid (CSF). 

Utilizing Seer's proprietary engineered nanoparticle technology, the system enables enrichment of a broad range of proteins across a wide dynamic range of abundances, improving the detection of low-abundance proteins that are often masked by highly abundant proteins. 

The SP200 automates nanoparticle-based protein capture and sample preparation, improving reproducibility, reducing hands-on time, and supporting high-throughput proteomic workflows.

In its current setup, the Proteograph SP200 is used for automated plasma and CSF sample preparation to support deep proteome profiling, biomarker discovery, and large-scale quantitative proteomic studies.

Coupled with high-resolution LC–MS/MS analysis using data-independent acquisition (DIA) on the Orbitrap Ascend Tribrid mass spectrometer, the current workflow enables the identification of approximately 3,000–4,000 proteins per plasma sample, depending on sample quality and experimental conditions.

Note: The PRF offers Proteograph-based biofluid profiling for projects with 40 or 80 samples per assay. For projects with fewer than 40 samples, please contact the Proteomics Resource Facility to discuss feasibility and available options before sample submission.