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Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

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Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
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Mass Analyzers: Common Types01:19

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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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Tandem Mass Spectrometry01:21

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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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Mass Analyzers: Overview01:13

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The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass...
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MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

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Mass spectrometry is a powerful characterization technique that can identify and separate a wide variety of compounds ranging from chemical to biological entities, based on their mass-to-charge ratio (m/z). The instruments that allow this detection, known as mass spectrometers, have three components: an ion source, a mass analyzer, and a detector. These spectrometers differ based on the nature of their ion source and analyzers.Matrix-assisted laser desorption ionization (MALDI) is a commonly...
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Mass Spectrometers

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This lesson details the instrumentation of a mass spectrometer—a physical instrument to perform mass spectrometry on analyte molecules and record the characteristic mass spectra. This is achieved via three chief functions:
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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

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MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics.

Nikita Prianichnikov1, Heiner Koch2, Scarlet Koch2

  • 1Computational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.

Molecular & Cellular Proteomics : MCP
|March 12, 2020
PubMed
Summary
This summary is machine-generated.

MaxQuant software now integrates ion mobility data, enhancing shotgun proteomics by improving proteome coverage and quantification accuracy. This 4D analysis boosts data analysis for complex biological samples.

Keywords:
Bioinformaticsbioinformatics softwarelabel-free quantificationmass spectrometryquantification

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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Computational Biology

Background:

  • Shotgun proteomics using LC-MS has limitations in proteome coverage and quantification.
  • Integrating ion mobility spectrometry (IMS) with LC-MS offers a fourth dimension (4D) for improved data analysis.
  • Specialized software is needed to process and extract information from this complex 4D data.

Purpose of the Study:

  • To introduce and describe the ion mobility-enhanced MaxQuant software for LC-IMS-MS/MS shotgun proteomics.
  • To present a computational workflow for peptide and protein identification and quantification using 4D data.
  • To demonstrate the software's utility with trapped ion mobility spectrometry (TIMS) coupled to a QTOF analyzer.

Main Methods:

  • Development of a parallelizable 4D feature detection algorithm for peak extraction and isotope pattern assembly.
  • Implementation of a non-linear mass recalibration model dependent on m/z, retention time, ion mobility, and signal intensity.
  • Introduction of a new matching between runs (MBR) algorithm utilizing collisional cross section (CCS) values for enhanced specificity and reduced missing values.

Main Results:

  • The ion mobility-enhanced MaxQuant software provides an end-to-end workflow for 4D proteomics data.
  • The CCS-aware MBR algorithm significantly improves specificity and reduces missing quantification values.
  • MS1 level label-free quantification demonstrates high precision and accuracy on benchmark datasets.

Conclusions:

  • Ion mobility-enhanced MaxQuant software effectively leverages the added dimension of ion mobility in LC-MS/MS data.
  • The software enhances proteome coverage, quantification accuracy, and dynamic range in shotgun proteomics.
  • This computational tool is a valuable asset for researchers analyzing complex proteomic samples using LC-IMS-MS/MS.