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

Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

You might also read

Related Articles

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

Sort by
Same author

Functional CRISPR screens reveal TPL1 lncRNA as a regulator of triple-negative breast cancer hallmarks.

Journal of advanced research·2026
Same author

Circulating Inflammation-Related Proteins Linked to Corneal Neuroimmune Measures, Neuropathy Deficits, and Symptoms in Type 2 Diabetes.

Journal of the peripheral nervous system : JPNS·2026
Same author

Proteomic profiling of tear fluid in patients with atopic keratoconjunctivitis.

The ocular surface·2026
Same author

Circulating proteomic markers are associated with measures of small and large fiber neuropathy and symptoms in type 2 diabetes.

Journal of diabetes and its complications·2026
Same author

Identification of Protein Signatures Reflecting Latent Variation in Aptamer-Based Affinity Proteomics.

Journal of proteome research·2026
Same author

LC-MS peptide mapping of monoclonal antibodies using the mirror proteases trypsin and Tryp-N.

Journal of pharmaceutical and biomedical analysis·2026

Related Experiment Video

Updated: Jun 26, 2026

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

Assembling proteomics data as a prerequisite for the analysis of large scale experiments.

Frank Schmidt1, Monika Schmid, Bernd Thiede

  • 1Max Planck Institute for Infection Biology, Core Facility Protein Analysis, Berlin, Germany. Frank.Schmidt@uni-greifswald.de

Chemistry Central Journal
|January 27, 2009
PubMed
Summary

A new database system, SQL-LIMS, effectively manages large-scale proteomics data from various instruments. This system unifies diverse data formats, enabling systematic analysis and reliable data validation for bacterial and protein complex studies.

More Related Videos

Analyzing Large Protein Complexes by Structural Mass Spectrometry
15:35

Analyzing Large Protein Complexes by Structural Mass Spectrometry

Published on: June 19, 2010

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Related Experiment Videos

Last Updated: Jun 26, 2026

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

Analyzing Large Protein Complexes by Structural Mass Spectrometry
15:35

Analyzing Large Protein Complexes by Structural Mass Spectrometry

Published on: June 19, 2010

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Area of Science:

  • Proteomics
  • Bioinformatics
  • Database Management

Background:

  • Bacterial genome sequencing is advanced, yet proteomes remain poorly defined.
  • Large-scale proteomics experiments require robust database applications for data storage and presentation.

Purpose of the Study:

  • To develop a database concept for managing and presenting large-scale proteomics data.
  • To address the need for unified data handling in proteomics workflows.

Main Methods:

  • Implemented an Oracle-based data repository system, SQL-LIMS, for proteomics workflows.
  • Utilized a Java-based data parser to store post-processed data from LC/ESI-MS, MALDI-MS, and 2-D gel electrophoresis (2-DE).
  • Transferred a subset of proteomics data to a public 2D-PAGE database adhering to PEDRo standardization.

Main Results:

  • SQL-LIMS successfully integrated and unified unique data formats from various instruments into standardized tables.
  • A unique submission identifier facilitated rapid access to all experimental data.
  • Data transfer via a Java-based Data Transfer Tool (DTT) enabled public data validation.

Conclusions:

  • SQL-LIMS serves as a comprehensive repository for managing large-scale, high-throughput proteomics experiments.
  • The system meets proteomics data handling requirements and PSI standardization criteria.
  • Post-processing of mass spectra improved data reliability and prevented storage of erroneous data.