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Related Concept Videos

Mass Analyzers: Common Types01:19

Mass Analyzers: Common Types

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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Optimizing Linear Ion-Trap Data-Independent Acquisition toward Single-Cell Proteomics.

Teeradon Phlairaharn1,2,3, Zilu Ye1, Elena Krismer1

  • 1The Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, København 2200, Denmark.

Analytical Chemistry
|June 20, 2023
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Summary
This summary is machine-generated.

Linear ion traps (LIT) can now perform comprehensive proteomics, including library generation, without relying on other mass analyzers. This advancement enables accurate quantification down to 0.5 ng for low-input samples and single-cell analysis.

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Area of Science:

  • Mass Spectrometry
  • Proteomics
  • Analytical Chemistry

Background:

  • Linear ion traps (LIT) offer affordability, robustness, and speed but have limitations in mass accuracy compared to time-of-flight or orbitrap analyzers.
  • Previous low-input proteomics studies using LITs often required complementary data from orbitrap instruments or orbitrap-based libraries.
  • This study explores the standalone capabilities of LITs for all mass spectrometry measurements in low-input proteomics.

Purpose of the Study:

  • To demonstrate the versatility of LIT as a stand-alone mass analyzer for low-input proteomics.
  • To optimize LIT data acquisition and library generation methods for sensitive and accurate proteomic analysis.
  • To evaluate the performance of LIT-based quantitative proteomics, including limits of quantification and single-cell applications.

Main Methods:

  • Optimization of LIT data acquisition parameters for proteomics.
  • Library-free database searches with and without entrapment peptides to assess detection and quantification.
  • Generation of matrix-matched calibration curves to determine the lower limit of quantification (LLOQ).
  • Development of a spectral library generation strategy for low-input samples.
  • Application of LIT-DIA (Data Independent Acquisition) for single-cell proteomics analysis using LIT-generated libraries.

Main Results:

  • LIT-MS1 measurements showed poor quantitative accuracy, while LIT-MS2 measurements achieved quantitative accuracy down to 0.5 ng on the column.
  • The lower limit of quantification was estimated using only 10 ng of starting material.
  • A robust spectral library generation strategy was optimized for low-input material.
  • Single-cell samples were successfully analyzed using LIT-DIA with libraries derived from as few as 40 cells.

Conclusions:

  • Linear ion traps can serve as versatile, stand-alone mass analyzers for comprehensive low-input proteomics, including library generation.
  • LIT-MS2 measurements provide accurate quantification crucial for analyzing minute biological samples.
  • This approach enables sensitive proteomic profiling of single cells, expanding the utility of affordable mass spectrometry platforms.