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

Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis14:48

Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis

7.6K
Here, we present an optimized on-filter digestion protocol with detailed information about the following: protein digestion, peptide purification and data independent acquisition analysis. This strategy is applied to the analysis of expressed prostatic secretions-urine samples and allows high proteome coverage and low missing value label-free profiling of the urinary proteome.
7.6K
Proteomic Analysis of Human Macrophage Polarization Under a Low Oxygen Environment10:15

Proteomic Analysis of Human Macrophage Polarization Under a Low Oxygen Environment

8.4K
We present a protocol to obtain proteomic signatures of human macrophages and apply this to determination of the impact of a low oxygen environment on macrophage...
8.4K
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes09:10

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

10.0K
Here we present the proteogenomic tool PoGo and protocols for fast, quantitative, post-translational modification and variant enabled mapping of peptides identified through mass spectrometry onto reference genomes. This tool is of use to integrate and visualize proteogenomic and personal proteomic studies interfacing with orthogonal genomics...
10.0K
Dissection of Human Retina and RPE-Choroid for Proteomic Analysis06:54

Dissection of Human Retina and RPE-Choroid for Proteomic Analysis

11.7K
The human retina is composed of functionally and molecularly distinct regions, including the fovea, macula, and peripheral retina. Here, we describe a method using punch biopsies and manual removal of tissue layers from a human eye to dissect and collect these distinct retinal regions for downstream proteomic...
11.7K
Enrichment of Extracellular Matrix Proteins from Tissues and Digestion into Peptides for Mass Spectrometry Analysis07:28

Enrichment of Extracellular Matrix Proteins from Tissues and Digestion into Peptides for Mass Spectrometry Analysis

28.3K
This protocol describes a procedure for enriching ECM proteins from tissues or tumors and deglycosylating and digesting the ECM-enriched preparations into peptides to analyze their protein composition by mass spectrometry.
28.3K
A Fluorogenic Peptide Cleavage Assay to Screen the Proteolytic Activity of Proteases02:42

A Fluorogenic Peptide Cleavage Assay to Screen the Proteolytic Activity of Proteases

562
This video demonstrates an assay to screen for the proteolytic activity of proteases using fluorogenic peptides. The protease recognizes its cleavage site on the peptide, cleaving it and separating the quencher from the fluorophore, enabling its fluorescence emission. The fluorescence signal is detected and analyzed to check for the cleavage efficiency of different peptide...
562

You might also read

Related Articles

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

Sort by
Same author

Association Between Upper Limb Injury and Risk of Falls: A Nationwide Population-Based Cohort Study.

Journal of clinical medicine·2026
Same author

Effect of antibiotic therapy versus no antibiotics on nonoperative management outcomes in uncomplicated appendicitis: A systematic review and meta-analysis.

International journal of colorectal disease·2026
Same author

Tubal ligation exacerbates ovulation-driven TP53 mutagenesis and p53 signatures by depleting protective menstrual hemoglobin.

The Journal of pathology·2026
Same author

Syphilis infection and incident dementia in two real-world cohorts: A harmonized propensity-matched analysis in Taiwan NHIRD and TriNetX Asia-Pacific.

Brain, behavior, and immunity·2026
Same author

Upper extremity fractures and subsequent total knee arthroplasty incidence in knee osteoarthritis: a cross-continental propensity score-matched cohort study.

Journal of orthopaedic surgery and research·2026
Same author

Nationwide cohort analysis of pediatric urolithiasis: long-term metabolic, renal, and cardiovascular outcomes.

Pediatric nephrology (Berlin, Germany)·2026

Related Experiment Video

Updated: Jan 20, 2026

Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis
14:48

Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis

Published on: May 8, 2021

7.6K

iHPDM: In Silico Human Proteome Digestion Map with Proteolytic Peptide Analysis and Graphical Visualizations.

Wai-Kok Choong1, Ching-Tai Chen1, Jen-Hung Wang1

  • 1Institute of Information Science , Academia Sinica , Taipei 11529 , Taiwan.

Journal of Proteome Research
|August 21, 2019
PubMed
Summary

Selecting the right protease is key for proteomics. The in silico Human Proteome Digestion Map (iHPDM) aids researchers in choosing proteases for identifying missing proteins and isoforms via mass spectrometry.

Keywords:
C-HPPiHPDMisoform digestionmissing proteinsprotease digestionproteolytic peptidesunique peptides

More Related Videos

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

10.0K
Dissection of Human Retina and RPE-Choroid for Proteomic Analysis
06:54

Dissection of Human Retina and RPE-Choroid for Proteomic Analysis

Published on: November 12, 2017

11.7K

Related Experiment Videos

Last Updated: Jan 20, 2026

Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis
14:48

Proteomic Profile of EPS-Urine through FASP Digestion and Data-Independent Analysis

Published on: May 8, 2021

7.6K
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

10.0K
Dissection of Human Retina and RPE-Choroid for Proteomic Analysis
06:54

Dissection of Human Retina and RPE-Choroid for Proteomic Analysis

Published on: November 12, 2017

11.7K

Area of Science:

  • Proteomics
  • Bioinformatics
  • Mass Spectrometry

Background:

  • Trypsin is the standard protease for proteomics, but it has limitations in identifying all proteins and isoforms.
  • Identifying unique peptides is crucial for accurate protein identification in mass spectrometry.

Purpose of the Study:

  • To develop a web-based resource, the in silico Human Proteome Digestion Map (iHPDM), to aid in protease selection for proteomics experiments.
  • To provide a comprehensive database of in silico digested human proteome peptides using various protease combinations.

Main Methods:

  • Constructed a proteolytic peptide database from human proteins and isoforms in neXtProt.
  • Utilized 15 combinations of one or two proteases for in silico digestion.
  • Developed user-friendly functions for examining, comparing, and filtering digestion results based on peptide properties.

Main Results:

  • Created a comprehensive database of in silico digested human proteome peptides.
  • The iHPDM allows users to compare digestion outcomes from different protease combinations.
  • Users can apply filters for peptide length and uniqueness to optimize protease selection.

Conclusions:

  • The iHPDM facilitates informed protease selection for shotgun proteomics.
  • This resource aids in the identification of missing proteins, protein isoforms, and single amino acid variant peptides.
  • iHPDM enhances the efficiency and scope of human proteome analysis.