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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Although all next-generation methods use different technologies, they all share a set of standard features.
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...
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...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

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Updated: Jun 17, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
10:37

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

Published on: November 15, 2017

De novo sequencing methods in proteomics.

Christopher Hughes1, Bin Ma, Gilles A Lajoie

  • 1Department of Biochemistry, University of Western Ontario, London, ON, Canada.

Methods in Molecular Biology (Clifton, N.J.)
|December 17, 2009
PubMed
Summary
This summary is machine-generated.

De novo sequencing of peptides using mass spectrometry offers a powerful computational approach to determine peptide sequences directly from experimental data. This method is crucial for identifying unknown proteins and is unaffected by database errors.

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Last Updated: Jun 17, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications
05:41

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications

Published on: July 10, 2020

Area of Science:

  • Proteomics
  • Computational Biology
  • Analytical Chemistry

Background:

  • Tandem mass spectrometry (MS/MS) is a key technology for peptide identification.
  • Traditional peptide identification relies on database searching, which can be limited by database completeness and accuracy.
  • De novo sequencing provides an alternative approach for peptide sequence determination.

Purpose of the Study:

  • To review and discuss de novo sequencing methods for peptides using mass spectrometry.
  • To highlight the advantages of de novo sequencing over database searching.
  • To explore the applications of de novo sequencing in various biological contexts.

Main Methods:

  • Computational analysis of experimental MS/MS spectra to deduce peptide sequences.
  • Discussion of various de novo sequencing algorithms and their underlying principles.
  • Comparison with database searching methods in tandem mass spectrometry.

Main Results:

  • De novo sequencing enables direct deduction of peptide sequences from MS/MS spectra.
  • These methods are essential for identifying proteins in organisms with unknown genomes.
  • De novo sequencing is robust against errors present in genomic or protein databases.

Conclusions:

  • De novo sequencing is a vital tool in proteomics, especially when genomic data is unavailable.
  • The method offers advantages even with known genomes, bypassing database limitations.
  • Partial sequences obtained from de novo sequencing facilitate the identification of post-translational modifications and mutations.