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Tandem Mass Spectrometry

Tandem Mass Spectrometry

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...

Peptide Identification Using Tandem Mass Spectrometry

Peptide Identification Using Tandem Mass Spectrometry

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.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

Mass Spectrometry: Overview

Mass Spectrometry: Overview

Mass spectrometry is an analytical technique used to determine the molecular mass and molecular formula of a compound. The basic principle of mass spectrometry is to generate ions from the analyte molecule and measure these ion abundances against their molecular mass. One common type of ionization, known as electron ionization or EI, bombards the analyte molecules in the gas phase with high-energy electron beams. The electron beams displace an electron from the molecule and leave behind a...

Mass Spectrometry: Complex Analysis

Mass Spectrometry: Complex Analysis

Mass spectrometry is an important technique for the identification of pure compounds. However, it has some limitations for the analysis of complex mixtures, often due to excessive fragmentation making the spectrum too complicated to decipher. Mass spectrometry can be combined with suitable separation methods in sequence, forming hyphenated methods, which are useful in the analysis of complex mixtures.
GC–MS is a powerful hyphenated method commonly used in forensics and environmental...

Mass Spectrometers

Mass Spectrometers

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High-Resolution Mass Spectrometry (HRMS)

High-Resolution Mass Spectrometry (HRMS)

The resolution of a mass spectrometer depends on the efficiency of separating ions with different ion masses. The mass of an atom is approximated to the sum of the masses of protons and neutrons inside, considering the masses of protons and neutrons as equal. However, the masses of the proton (1.6726 × 10−24 g) and neutron (1.6749 × 10−24 g) are not truly equal. There is a minor error in the expression of atomic masses relative to the simplest atom of hydrogen. For example, the mass of helium...

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Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments

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Published on: January 20, 2022

SwissPIT: An workflow-based platform for analyzing tandem-MS spectra using the Grid.

Andreas Quandt¹, Alexandre Masselot, Patricia Hernandez

¹Swiss Institute of Bioinformatics, Proteome Informatics Group, Geneva, Switzerland. andreas.quandt@isb-sib.ch

|April 25, 2009

Summary

The Swiss protein identification toolbox (swissPIT) offers a unified platform for automated MS data analysis. It addresses limitations in current proteomics software, improving peptide identification from MS/MS spectra.

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Area of Science:

Proteomics and Bioinformatics
Computational Biology

Background:

Peptide identification from MS/MS data is crucial in proteomics.
Existing bioinformatics tools often use single programs with fixed parameters, leading to suboptimal results.
Inconsistent input/output formats and lack of unified visualization hinder data analysis.

Purpose of the Study:

To introduce the Swiss protein identification toolbox (swissPIT) as a comprehensive solution for MS/MS data analysis.
To overcome limitations of existing proteomics software by providing a flexible and automated platform.
To enhance the accuracy and efficiency of peptide and protein identification.

Main Methods:

Development of the swissPIT platform, integrating multiple identification programs and search strategies.
Implementation of standardized input/output formats and a unified result visualization system.
Utilization of a distributed computing Grid (Swiss-wide computer Grid) for handling intensive calculations.

Main Results:

swissPIT provides an expandable multitool for automated, in-depth MS data analysis.
The platform addresses challenges in data format standardization, workflow creation, result visualization, and user interface simplicity.
Currently supports four programs with two distinct search strategies for MS/MS spectra identification.

Conclusions:

swissPIT offers a robust and user-friendly solution for proteomics data analysis.
The integrated approach enhances the reliability and scope of peptide identification from MS/MS spectra.
The platform is designed for high-throughput experiments and leverages distributed computing resources.