Mass Spectrometry Core Facility Guide
How to choose the right mass spectrometry facility for your proteomics, metabolomics, or structural biology project.
Choosing the Right Instrument
The Orbitrap Astral is the current gold standard for deep proteome coverage with unmatched speed. The timsTOF Ultra excels at 4D proteomics with TIMS ion mobility. The Orbitrap Eclipse Tribrid is the most versatile for multi-mode experiments. Your choice depends on sample type, throughput needs, and the specific experiment.
DDA vs. DIA Workflows
Data-Dependent Acquisition (DDA) is the traditional approach, selecting precursors in real-time for fragmentation. Data-Independent Acquisition (DIA) fragments everything in predefined windows, providing more reproducible quantification. Most modern facilities support both, but some specialize in one or the other.
Sample Submission Requirements
Facilities typically require: purified peptide digests (for bottom-up proteomics), intact proteins in MS-compatible buffer (for top-down), or metabolite extracts in appropriate solvent. Many facilities offer sample preparation services for an additional fee. Always consult with the facility before preparing samples.
Frequently Asked Questions
What is the difference between Orbitrap and timsTOF?
Orbitrap instruments trap ions in an electrostatic field and measure m/z from oscillation frequency, offering very high resolution. timsTOF adds trapped ion mobility spectrometry (TIMS) for an additional separation dimension, improving peak capacity and sensitivity for complex samples.
Need Help Finding a Facility?
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