Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

8.1K
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...
8.1K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

20.5K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
20.5K
MALDI-TOF Mass Spectrometry01:19

MALDI-TOF Mass Spectrometry

6.5K
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...
6.5K
Tandem Mass Spectrometry01:21

Tandem Mass Spectrometry

2.3K
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...
2.3K
Mass Spectrometry: Molecular Fragmentation Overview01:20

Mass Spectrometry: Molecular Fragmentation Overview

5.4K
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...
5.4K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Fungal Extracellular Vesicles are Recoverable Across Variable Ultracentrifugation Speeds but Display Species-specific Profiles of Sedimentation.

The Journal of membrane biology·2026
Same author

Cellular and molecular responses of <i>Cryptococcus</i> to brilacidin.

Microbiology spectrum·2026
Same author

Single-cell proteomics: When individual cells tell population stories.

Trends in biochemical sciences·2026
Same author

Comparative omics reveals conserved extracellular matrix signatures during mammary tumor progression.

Frontiers in oncology·2026
Same author

Quinoa bioester application shifts human skin proteome toward molecular profiles associated with younger age.

Communications biology·2026
Same author

Human milk oligosaccharides promote synaptogenesis and neurite outgrowth in human cortical organoids.

Biochemistry and biophysics reports·2026

Related Experiment Video

Updated: Jan 15, 2026

Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry CCMS
17:12

Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry CCMS

Published on: December 20, 2010

16.0K

SequenceAssembler: A tool for protein sequence assembly from mass spectrometry data.

Celso Vitor A Q Calomeno1, Hulyana Brum2, Rodrigo S C Brant3

  • 1Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz Paraná, Paraná, Brazil.

Journal of Proteomics
|October 10, 2025
PubMed
Summary

SequenceAssembler (SA) software integrates peptide-spectrum matching and de novo sequencing data to reconstruct full-length proteins. This user-friendly tool enhances protein sequencing for biological research and biopharmaceutical development.

Keywords:
BioinformaticsMass spectrometryProtein sequencing assemblyProteomics

More Related Videos

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

9.1K
Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

845

Related Experiment Videos

Last Updated: Jan 15, 2026

Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry CCMS
17:12

Profiling of Methyltransferases and Other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry CCMS

Published on: December 20, 2010

16.0K
Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

9.1K
Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

845

Area of Science:

  • Proteomics
  • Biotechnology
  • Biopharmaceutical Development

Background:

  • Accurate sequencing of complete proteoforms is crucial for understanding biological systems and advancing drug development.
  • Current methods may lack integration for comprehensive protein sequence assembly.

Purpose of the Study:

  • To introduce SequenceAssembler (SA), a software tool for assembling full-length protein sequences.
  • To integrate peptide-spectrum matching (PSM) and de novo sequencing data for enhanced protein reconstruction.

Main Methods:

  • Developed SequenceAssembler (SA) software with a user-friendly graphical interface.
  • Integrated SA with established proteomics tools (Novor Cloud, PEAKS Studio, PatternLab for Proteomics).
  • Validated SA by analyzing bovine serum albumin and trastuzumab using high-resolution mass spectrometry.

Main Results:

  • SA successfully assembled full-length protein sequences by combining PSM and de novo sequencing data.
  • Performance was comparable to existing tools like Stitch, with results dependent on parameter thresholds.
  • Demonstrated ease of use with a streamlined workflow and one-click installation.

Conclusions:

  • SequenceAssembler provides a unified platform for protein sequence assembly, addressing a gap in proteomics.
  • The intuitive interface lowers adoption barriers, improving reproducibility and efficiency in core laboratories.
  • SA facilitates rapid protein sequencing for diverse research applications.