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Tandem mass spectrometry is a technique that uses multiple mass analyzers in series to obtain a higher selectivity and reduce chemical noise during analyte detection. Instruments with multiple analyzers separated by an interaction cell enable secondary fragmentation and selected study of the fragment ions.Secondary fragmentations occur in the interaction cell and can be induced by various factors. Fragmentation induced by collision with inert gases, such as N2, Ar, He, etc., is called...
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Plasma Proteomics Across Three Generations of Mass Spectrometry Instruments: Lessons for Biofluid Method

Jack Edwards1,2,3, Dylan H Multari1,2,4, Toby Dite1,2,5

  • 1Advanced Technology and Biology Division, Walter and Eliza Hall Institute, Parkville, Victoria, Australia.

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Summary
This summary is machine-generated.

Benchmarking liquid chromatography (LC) and data-independent acquisition (DIA) methods across three mass spectrometry (MS) generations revealed instrument-specific optimization strategies for plasma proteomics. Tailored method development enhances low-abundance biomarker detection in clinical samples.

Keywords:
astralautomatic gain controlclinical proteomicsdata‐independent acquisitionorbitrapplasma proteomicsquantitation

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Area of Science:

  • Proteomics
  • Biomarker Discovery
  • Analytical Chemistry

Background:

  • Plasma proteomics is crucial for biomarker discovery, but high-abundance proteins mask low-abundance biomarkers.
  • Existing workflows often focus on sample preparation, yet mass spectrometry (MS) method optimization significantly impacts detection.
  • Technological advancements in MS instruments offer potential for improved plasma proteomic analysis.

Purpose of the Study:

  • To benchmark liquid chromatography (LC) and data-independent acquisition (DIA) methods across three generations of mass spectrometry instruments.
  • To evaluate the impact of LC-MS method variations on plasma proteomic analysis.
  • To assess the quantitative accuracy and sensitivity of different MS instruments for low-abundance peptide detection.

Main Methods:

  • Benchmarking of 27 LC-MS method combinations across three MS instrument generations (timsTOF Pro, Orbitrap Eclipse, Orbitrap Astral).
  • Evaluation of instrument performance using a mixture of platelet-poor plasma (PPP) and platelet-rich plasma (PRP) to create linear contamination markers.
  • Testing of Orbitrap Astral's parallel ion processing and gas-phase enrichment (GPE) capabilities.

Main Results:

  • Each instrument generation showed improved performance, with unique tuneable ranges for plasma samples.
  • Plasma-specific method development is beneficial for optimizing mass spectrometer performance.
  • The PPP/PRP mixture approach effectively tested sensitivity and quantitative accuracy for low-abundance peptides.
  • Optimization of MS2 AGC targets and injection time enhanced GPE, improving low-abundance peptide detection on the Orbitrap Astral.

Conclusions:

  • Mass spectrometry instrument performance in plasma proteomics has significantly advanced across generations.
  • Instrument-specific method optimization, particularly for LC-MS and DIA, is essential for maximizing biomarker discovery potential.
  • Advanced techniques like gas-phase enrichment show promise for enhancing the detection of low-abundance proteins in complex matrices like plasma.