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

8.8K
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...
8.8K
Translocation of Proteins into the Mitochondria01:19

Translocation of Proteins into the Mitochondria

13.6K
Mitochondrial precursors are translocated to the internal subcompartments via independent mechanisms involving distinct protein machineries called translocases.
Sorting of outer membrane proteins:
Mitochondrial outer membrane proteins are of two types: the transmembrane, beta-barrel porins, and the membrane-anchored, alpha-helical proteins. Beta-barrel porin precursors are translocated by the TOM complex and inserted into the outer mitochondrial membrane by the SAM complex. In contrast,...
13.6K

You might also read

Related Articles

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

Sort by
Same author

Spatial distribution of the proteome in the human body and in cancers.

Nature·2026
Same author

Integrated proteogenomic and metabolomic profiling of acute myeloid leukemias to identify molecular subtypes and associated therapy targets.

Nature cancer·2026
Same author

Small-molecule binding-site discovery using silyl ether-enabled chemoproteomics.

Nature chemistry·2026
Same author

Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.

Nature communications·2026
Same author

Expanding Glycopeptide Identification with Match-Between-Glycans in FragPipe.

bioRxiv : the preprint server for biology·2026
Same author

iPepGen: a modular, immunopeptidogenomic analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates.

Genome biology·2026
Same journal

From Method-Defined Signals to Reference Measurement Procedures: Two Decades of Mass Spectrometry-Based ProGRP Quantification.

Journal of proteome research·2026
Same journal

Proteomic Profiling of Extracellular Vesicle-Enriched Plasma Using Mag-Net for Biomarker Discovery in Pancreatic Ductal Adenocarcinoma.

Journal of proteome research·2026
Same journal

Computationally Efficient Bayesian Estimation of Graphical Networks for Omics Data.

Journal of proteome research·2026
Same journal

Hierarchy of MS-Based Evidence.

Journal of proteome research·2026
Same journal

Proteomic Profiling of Exosomes from HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinoma: Selective Cargo Packaging.

Journal of proteome research·2026
Same journal

Proteomic Analysis Identifies ATE1-Dependent Arginylation Dysregulation across Meningioma Grades.

Journal of proteome research·2026
See all related articles

Related Experiment Video

Updated: Mar 13, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.7K

PIPI: PTM-Invariant Peptide Identification Using Coding Method.

Fengchao Yu1, Ning Li1,2, Weichuan Yu1,3

  • 1Division of Biomedical Engineering, The Hong Kong University of Science and Technology , Hong Kong, China.

Journal of Proteome Research
|October 18, 2016
PubMed
Summary
This summary is machine-generated.

PIPI is a novel computational method for identifying peptides with post-translational modifications (PTMs). It efficiently handles unlimited PTM types, offering high sensitivity and accuracy in proteomics research.

Keywords:
database searchpeptide identificationunrestricted PTM identification

More Related Videos

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics
09:09

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics

Published on: October 13, 2020

5.2K
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

10.1K

Related Experiment Videos

Last Updated: Mar 13, 2026

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.7K
Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics
09:09

Semi-Quantitative Analysis of Peptidoglycan by Liquid Chromatography Mass Spectrometry and Bioinformatics

Published on: October 13, 2020

5.2K
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

10.1K

Area of Science:

  • Computational proteomics
  • Bioinformatics
  • Mass spectrometry data analysis

Background:

  • Identifying peptides with post-translational modifications (PTMs) is crucial but computationally challenging.
  • Existing methods are either restricted in PTM types or suffer from low sensitivity due to large search spaces.
  • Accurate PTM localization and characterization are essential for understanding protein function.

Purpose of the Study:

  • To develop a novel computational method, PIPI, for PTM-invariant peptide identification.
  • To improve the sensitivity and accuracy of peptide identification in the presence of diverse PTMs.
  • To provide an efficient unrestricted tool for computational proteomics.

Main Methods:

  • PIPI codes peptide sequences into Boolean vectors and experimental spectra into real-valued vectors.
  • It searches a coded sequence database to identify candidate peptides.
  • Dynamic programming is employed for PTM localization and characterization within candidate peptides.

Main Results:

  • PIPI demonstrates comparable sensitivity and running speed to restricted tools.
  • Among unrestricted tools, PIPI shows high sensitivity, outperforming most except those simplifying PTM analysis.
  • PIPI achieves the lowest false discovery proportion and highest PTM characterization accuracy among unrestricted tools.

Conclusions:

  • PIPI is an effective unrestricted tool for PTM-invariant peptide identification.
  • The method offers a balance of high sensitivity, accuracy, and computational efficiency.
  • PIPI advances computational proteomics by enabling robust analysis of complex PTM patterns.