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Updated: Jun 20, 2026
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Database on Demand - an online tool for the custom generation of FASTA-formatted sequence databases
Florian Reisinger1, Lennart Martens
1EMBL Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
Proteomics
|September 3, 2009
Summary
Customized search databases enhance mass spectrometry-based proteomics by enabling in silico peptide identification beyond standard digestion. Database on Demand offers a user-friendly web tool for creating diverse, tailored search databases for improved proteomic analysis.
Area of Science:
- Proteomics
- Bioinformatics
- Mass Spectrometry
Background:
- Mass spectrometry-based proteomics relies on matching spectral data to sequence databases for peptide identification.
- Conventional search engines often use standard digestion algorithms, limiting the scope of in silico peptide derivation.
- Optimizing search databases is crucial for accurate and comprehensive proteomic analysis, particularly in complex experiments like gel-free proteomics.
Purpose of the Study:
- To introduce Database on Demand, a novel web tool for generating customized search databases.
- To provide researchers with enhanced control over the search space for mass spectrometry-based proteomics.
- To improve the performance of peptide identification in proteomics experiments through tailored databases.
Main Methods:
- Development of an easy-to-use web-based platform named Database on Demand.
- Implementation of functionalities for creating a wide variety of customized search databases.
- Focus on enabling customized in silico peptide derivation beyond standard digestion algorithms.
Main Results:
- Database on Demand allows for the rapid production of customized search databases.
- The tool offers detailed control over the search space, surpassing standard strategies.
- Facilitates improved peptide identification in mass spectrometry-based proteomics.
Conclusions:
- Customized search databases significantly enhance the capabilities of mass spectrometry-based proteomics.
- Database on Demand provides a valuable and accessible resource for researchers seeking to optimize their proteomic analyses.
- The tool empowers scientists to generate bespoke databases, leading to more accurate and comprehensive peptide identifications.
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