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

6.4K
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...
6.4K

You might also read

Related Articles

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

Sort by
Same author

gSV: a general structural variant detector using the third-generation sequencing data.

Briefings in bioinformatics·2026
Same author

Direct inference of haplotypes from sequencing data.

Bioinformatics advances·2025
Same author

BVSim: A benchmarking variation simulator mimicking human variation spectrum.

GigaScience·2025
Same author

epLSAP-Align: a non-sequential protein structural alignment solver with entropy-regularized partial linear sum assignment problem formulation.

Bioinformatics (Oxford, England)·2025
Same author

Exhaustive Cross-Linking Search with Protein Feedback.

Journal of proteome research·2022
Same author

Region-based interaction detection in genome-wide case-control studies.

BMC medical genomics·2020

Related Experiment Video

Updated: Jun 25, 2025

A Spin-Tip Enrichment Strategy for Simultaneous Analysis of N-Glycopeptides and Phosphopeptides from Human Pancreatic Tissues
09:16

A Spin-Tip Enrichment Strategy for Simultaneous Analysis of N-Glycopeptides and Phosphopeptides from Human Pancreatic Tissues

Published on: May 4, 2022

2.2K

PIPI2: Sensitive Tag-Based Database Search to Identify Peptides with Multiple Post-translational Modifications.

Shengzhi Lai1, Peize Zhao2, Chen Zhou1

  • 1Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, Hong Kong, China.

Journal of Proteome Research
|May 21, 2024
PubMed
Summary

PIPI2, a new open search engine, significantly improves peptide identification and post-translational modification (PTM) characterization in proteomics. It excels at identifying peptides with multiple PTMs, outperforming existing methods in both accuracy and precision.

Keywords:
bottom-up proteomicspost-translational modificationtag-based database searchtandem mass spectrometry

More Related Videos

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides
08:37

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides

Published on: November 2, 2021

2.2K
Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry
11:54

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

9.5K

Related Experiment Videos

Last Updated: Jun 25, 2025

A Spin-Tip Enrichment Strategy for Simultaneous Analysis of N-Glycopeptides and Phosphopeptides from Human Pancreatic Tissues
09:16

A Spin-Tip Enrichment Strategy for Simultaneous Analysis of N-Glycopeptides and Phosphopeptides from Human Pancreatic Tissues

Published on: May 4, 2022

2.2K
The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides
08:37

The Application of Open Searching-based Approaches for the Identification of Acinetobacter baumannii O-linked Glycopeptides

Published on: November 2, 2021

2.2K
Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry
11:54

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

9.5K

Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Biochemistry

Background:

  • Peptide identification is essential for bottom-up proteomics.
  • Post-translational modifications (PTMs) regulate cellular functions.
  • Identifying peptides with PTMs is challenging, especially with multiple modifications.

Purpose of the Study:

  • To develop a sensitive open search engine for improved peptide identification with PTMs.
  • To enhance the characterization precision of multiple PTMs on peptides.
  • To present PIPI2 as a superior tool for handling complex PTM patterns.

Main Methods:

  • Developed PIPI2, a sensitive open search engine.
  • Employed a greedy approach to simplify PTM characterization into a linear problem.
  • Tested performance on simulated datasets with up to four PTMs per peptide.

Main Results:

  • PIPI2 identified over 90% of spectra on simulated data, exceeding competitors by at least 56%.
  • Achieved the highest PTM pattern characterization precision at 77%.
  • Identified 30% to 88% more peptides with PTMs in real applications compared to competitors.

Conclusions:

  • PIPI2 demonstrates superior performance in identifying peptides with multiple PTMs.
  • The tool offers significant advantages in handling complex PTM patterns.
  • PIPI2 enhances both the identification rate and characterization precision of PTMs in proteomics.