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Related Concept Videos

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
Tandem Mass Spectrometry01:21

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 Spectrometry01:33

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: Overview01:19

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 Analysis01:21

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 Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

The ionization of a molecule into a molecular ion inside the mass spectrometer causes instability in the molecule's structure due to the loss of an electron. This eventually leads to the fragmentation or breaking of some bonds in the molecule. The fragmentation occurs predominantly at specific bonds to yield relatively stable fragments.
One type of fragmentation pattern is the cleavage of a single bond in the molecular ion. The cleavage leads to a radical and a cation. The cleavage can occur at...

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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

Published on: August 19, 2025

MASPECTRAS 2: An integration and analysis platform for proteomic data.

Ceereena Ubaida Mohien1, Jürgen Hartler, Florian Breitwieser

  • 1Institute for Genomics and Bioinformatics, Graz University of Technology, Austria.

Proteomics
|May 11, 2010
PubMed
Summary
This summary is machine-generated.

MASPECTRAS 2 integrates mass spectrometry protein identifications with bioinformatics data, aiding researchers in data interpretation and publication. This platform supports high-throughput analysis and data sharing for proteomics research.

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Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling
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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
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Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

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Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling
09:35

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Published on: April 1, 2017

Area of Science:

  • Bioinformatics
  • Proteomics
  • Computational Biology

Background:

  • Mass spectrometry (MS) generates large protein identification datasets.
  • Integrating MS data with diverse bioinformatics resources is crucial for interpretation.
  • Existing platforms may lack comprehensive integration or high-throughput capabilities.

Purpose of the Study:

  • To introduce MASPECTRAS 2, a platform for integrating MS protein identifications with major bioinformatics databases.
  • To enhance data understanding, facilitate publication, and support high-throughput analysis in proteomics.
  • To demonstrate the utility of MASPECTRAS 2 using tyrosine kinase inhibitor drug proteomics data.

Main Methods:

  • Integration of MS protein identifications with ontologies, domains, and literature databases.
  • Implementation of features for sample comparisons, targeted queries, summaries, and exports (e.g., PRIDE XML).
  • Development of mechanisms for integration into high-throughput analysis infrastructures.

Main Results:

  • MASPECTRAS 2 provides a unified platform for accessing and analyzing proteomics data.
  • The platform facilitates data interpretation and supports publication through various analytical tools.
  • Successful application demonstrated with unpublished tyrosine kinase inhibitor drug proteomics profiles.

Conclusions:

  • MASPECTRAS 2 is a valuable, freely available resource for the proteomics research community.
  • The platform enhances the utility of MS-based proteomics data through comprehensive integration and analysis tools.
  • MASPECTRAS 2 is suitable for both individual research and high-throughput applications.