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Related Concept Videos

Proteomics01:33

Proteomics

7.7K
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...
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Protein Modifications in the RER01:26

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Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
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Mass Spectrometry: Overview01:19

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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 electrospray 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...
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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.
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...
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Mass Spectrometry: Complex Analysis01:21

Mass Spectrometry: Complex Analysis

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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...
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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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A Python Package for the Localization of Protein Modifications in Mass Spectrometry Data.

Anthony S Barente1, Judit Villén1

  • 1Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States.

Journal of Proteome Research
|October 31, 2022
PubMed
Summary

pyAscore is a new Python tool for pinpointing post-translational modifications (PTMs) on peptides. This open-source package enhances mass spectrometry data analysis for proteomics research.

Keywords:
Pythoncomputationphosphorylationpost-translational modificationsite localizationsoftware

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Area of Science:

  • Proteomics
  • Computational Biology
  • Biochemistry

Background:

  • Accurate localization of post-translational modifications (PTMs) is crucial for understanding protein function.
  • Existing PTM localization algorithms are often limited to standalone applications or software suites.
  • Enhanced accessibility and versatility are needed for integrating these algorithms into diverse research workflows.

Purpose of the Study:

  • To introduce pyAscore, a Python implementation of the Ascore algorithm.
  • To provide a versatile tool for scoring PTM localization in mass spectrometry data.
  • To facilitate the integration of PTM analysis into custom bioinformatics pipelines.

Main Methods:

  • Developed pyAscore as an open-source Python package (Python 3.6+).
  • Implemented the Ascore algorithm for efficient PTM localization scoring.
  • Ensured compatibility with standard file formats from popular proteomics software.
  • Enabled command-line and Python script usage.

Main Results:

  • pyAscore offers an efficient and versatile solution for PTM localization.
  • The tool accepts standard input formats, facilitating broad applicability in bottom-up proteomics.
  • Provides access to internal scoring objects for advanced PTM analysis within Python.

Conclusions:

  • pyAscore enhances the analysis of post-translational modifications in proteomics.
  • Its Python implementation and versatility promote wider adoption and integration into research.
  • The open-source package is readily available for various operating systems.