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

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

11.3K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
11.3K
Protein-protein Interfaces02:04

Protein-protein Interfaces

13.1K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
13.1K
Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

3.8K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
3.8K
Protein Networks02:26

Protein Networks

4.1K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.1K
Conservation of Protein Domains02:26

Conservation of Protein Domains

3.2K
3.2K
Protein Families02:47

Protein Families

15.7K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
15.7K

You might also read

Related Articles

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

Sort by
Same author

Impact of depression on treatment response and survival among patients with breast cancer: A multi-institutional retrospective cohort study.

Breast (Edinburgh, Scotland)·2026
Same author

Metabolic profiling of DNA methylation age acceleration, associations with hearing loss and interaction with genetic susceptibility.

Free radical biology & medicine·2026
Same author

Diastereomer separation of phosphorothioate oligonucleotides via conformationally stabilizing ion pairs in reversed-phase liquid chromatography.

Journal of chromatography. A·2026
Same author

Rethinking bioinformatics expertise in the era of artificial intelligence.

NPJ digital medicine·2026
Same author

[The SCD diagnostic strategy, procedure and pathway for episodic vestibular syndrome].

Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery·2026
Same author

[Surgical treatment of Meniere's disease].

Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery·2026

Related Experiment Video

Updated: Sep 5, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.8K

Resolving missing protein problems using functional class scoring.

Bertrand Jern Han Wong1, Weijia Kong1,2,3, Limsoon Wong2

  • 1School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.

Scientific Reports
|July 5, 2022
PubMed
Summary
This summary is machine-generated.

The missing protein problem (MPP) in proteomics is addressed by Functional Class Scoring (FCS). FCS effectively recovers missing proteins, even with recent technologies like SWATH-DIA, improving biomarker discovery.

More Related Videos

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.4K
An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.5K

Related Experiment Videos

Last Updated: Sep 5, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.8K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.4K
An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.5K

Area of Science:

  • Proteomics
  • Bioinformatics
  • Systems Biology

Background:

  • Proteomics studies face incomplete coverage and inconsistencies, leading to the missing protein problem (MPP).
  • The MPP hinders accurate biomarker discovery and protein functional characterization.
  • Network-based approaches offer solutions, with Functional Class Scoring (FCS) leveraging protein complex data.

Purpose of the Study:

  • To rigorously evaluate FCS performance on modern proteomic data, specifically Data-Independent Acquisition (DIA) technologies.
  • To develop a robust evaluation framework for assessing methods addressing the MPP.
  • To validate the biological relevance and statistical significance of proteins predicted by FCS.

Main Methods:

  • Devised a novel evaluation schema using cross-verification between technical replicates.
  • Applied FCS to proteomic data acquired using SWATH-DIA technology.
  • Assessed the statistical significance of predicted missing proteins using FCS p-values.

Main Results:

  • FCS successfully identifies biologically meaningful networks, indicated by conserved tissue-specific signals despite some technical replicate inconsistencies.
  • Predicted missing proteins are statistically significant and, as a group, show higher peptide support than non-predicted proteins.
  • FCS effectively recovers proteins that might otherwise be missed due to weak peptide evidence.

Conclusions:

  • FCS is a valuable tool for resolving the missing protein problem in high-coverage proteomics, including DIA data.
  • The developed evaluation schema provides a rigorous method for assessing missing protein prediction tools.
  • FCS enhances the completeness and reliability of proteomic datasets for downstream analyses.