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Mass Analyzers: Common Types

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The quadrupole mass analyzer consists of four cylindrical metal rods arranged in a diamond carrying a DC voltage and a radio-frequency AC voltage. The motion of ions through the quadrupole depends on the field strength, causing only ions of a certain m/z to resonate successfully and strike the detector at a given field strength. Though the transmission rate for these analyzers is high, the exact elemental composition of the sample is not determined because of low resolution; however, they are...

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Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

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Benchmarking the Orbitrap Tribrid Eclipse for Next Generation Multiplexed Proteomics.

Qing Yu¹, Joao A Paulo¹, Jose Naverrete-Perea¹

¹Harvard Medical School, Boston, Massachusetts 02115, United States.

Analytical Chemistry

|April 7, 2020

Summary

This summary is machine-generated.

New mass spectrometry hardware and software significantly improve quantitative proteomics. These advancements increase peptide identifications and throughput for complex biological sample comparisons without compromising accuracy.

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Area of Science:

Proteomics
Mass Spectrometry
Quantitative Biology

Background:

Quantitative proteomics is crucial for dissecting complex biological phenotypes.
Advancements in instrumentation and software are key to improving proteomic analysis.
Sample multiplexing strategies are increasingly used in comparative studies.

Purpose of the Study:

To evaluate the utility of the Orbitrap Eclipse Tribrid mass spectrometer and its new software features for quantitative proteomics.
To assess the impact of specific features like Precursor Fit filtering, TurboTMT, and Real-time Peptide Search on data acquisition and analysis.
To determine if enhanced sensitivity and identification rates affect quantitative accuracy.

Main Methods:

Utilized the Orbitrap Eclipse Tribrid mass spectrometer with advanced quadrupole filter and optimized FTMS scan overhead.
Implemented new instrument control software features: Precursor Fit filtering, TurboTMT, and Real-time Peptide Search filtering.
Performed multidimensional comparisons of these novel features using SPS-MS3 and HRMS2 methods.

Main Results:

Achieved a 20% increase in total peptide identifications for SPS-MS3 methods.
Observed a 14% increase in total peptide identifications for HRMS2 methods.
Real-time Peptide Search filtering resulted in approximately a 2x throughput improvement for quantification without sacrificing accuracy.

Conclusions:

The evaluated hardware and software features enhance the efficiency and depth of quantitative proteomics.
These advancements facilitate more comprehensive comparative proteome-wide insights.
The new capabilities support more robust dissection of complex phenotypic differences.