Welcome to CONGA’s documentation!

Contents:

• Output files
• Parameters
  • Neighbor filtration
  • Dynamic-level competition
  • Group construction
  • Group-walk algorithm
  • Localization scoring
  • CPU processes
  • Input and output
• Tutorial example
  • Crux-Tide
  • Comet
  • MSFragger
  • Interpreting the log file
• Limelight

Introduction

CONGA is a tool for discovering peptides in mass-spectrometry data with theoretical FDR control. It requires three inputs: (1) the set of top-1 PSMs per spectrum using a narrow-window search against a concatenated target-decoy database, (2) the set of top k PSMs (or less if fewer than k PSMs exist for a given spectrum) using an open search, again against a concatenated target-decoy database, and (3) the paired list of target and decoy peptide sequences from the database. Ideally, an additional option is set which specifies the isolation window used. Given this, CONGA will return a discovery list of peptides. CONGA is able to make simultaneous discoveries from both open- and narrow-search files, detect unaccounted for post-translational modifications of the sample peptides, and detect peptides generated by chimeric experimental spectra.

Links

• Source code: https://github.com/freejstone/CONGA

• Paper: To be added

• Search Page