TIDD

TIDD (Tool for Increasing Discriminability of Database search results) is a universal post-processing software tool to improve the confidence of peptide identifications in shotgun proteomics. It works with results from any database search engine, including newly developed ones, without needing search engine-specific optimization.

Key features of TIDD:

1. Universality: TIDD calculates universal features to assess the quality of peptide-spectrum matches (PSMs), making it compatible with search engine results.

2. Flexibility: Besides universal features, TIDD allows the incorporation of additional features provided by search engines or users.

3. Performance: Despite relying on universal features, TIDD demonstrates similar or better performance compared to Percolator, a popular post-processing tool, in terms of peptide identification.

4. Improved identification: TIDD identified 10.23-38.95% more PSMs than target-decoy estimation for MSFragger, a search engine not supported by Percolator.

5. User-friendly interface: TIDD offers a simple graphical user interface for ease of use.

Topic

Proteomics;Proteomics experiment;Small molecules;Machine learning

Detail

  • Operation: Target-Decoy;Tag-based peptide identification;de Novo sequencing

  • Software interface: Command-line interface. graphical user interface

  • Language: Java,R

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: National Research Foundation of Korea, Institute of Information & communications Technology Planning & Evaluation (IITP), Korea government (MSIT).

  • Input: -

  • Output: -

  • Contact: -

  • Collection: -

  • Maturity: -

Publications

  • TIDD: tool-independent and data-dependent machine learning for peptide identification.
  • Li H, et al. TIDD: tool-independent and data-dependent machine learning for peptide identification. TIDD: tool-independent and data-dependent machine learning for peptide identification. 2022; 23:109. doi: 10.1186/s12859-022-04640-y
  • https://doi.org/10.1186/S12859-022-04640-Y
  • PMID: 35354356
  • PMC: PMC8969291

Download and documentation

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