Modules

Here is a list of all modules:

• Installing Mascot Parser
  • Perl toolkit installation
  • C++ toolkit installation
    • C++ toolkit installation on Windows
    • C++ toolkit installation on Unix
  • Java toolkit installation
  • Python toolkit installation
  • C# toolkit installation
• Getting started with Mascot Parser
  • Quickstart: how to open a results file
  • Using the toolkit from C++
  • Using the toolkit from Perl, Java, Python and C#
  • Garbage collection problems (advanced reading)
  • Multithreading (advanced reading)
• Mascot results file module
  • Examples for the results file module
  • UML Class Diagram
  • Issues with backward compatibility for results files
  • Error Handling
  • Peptide mass fingerprint mixtures
  • Grouping proteins together
  • Unassigned peptides list
  • Treatment of duplicate peptides
  • Detecting ambiguous peptide matches
  • Error tolerant searches
  • Crosslinked search results
  • Using the singleHit parameter to return a single protein
  • Automated repeating of searches
  • Target-decoy searches and false discovery rate
  • Using Percolator scores
  • Caching Mascot Results
  • Combining multiple .dat files
  • Query-level modifications
  • Spectral libraries
  • Spectral library score threshold (advanced reading)
• Mascot configuration files module
  • Configuration files
  • Examples for the configuration files module
  • Fixed values for quantitation.xml
  • Fixed values for crosslinking.xml
• Mascot security and authentication module
  • Using the Mascot security module
  • Examples for the Mascot security module
• Mascot utilities and tools module
  • Examples for the Mascot tools module
  • Spectral library Classes
• Error handling and logging
  • Error Handling
  • Logging using ms_loggingmonitor
  • Examples for error handling in Mascot Parser modules
• Quantitation analysis for Mascot Server and Distiller
  • Peptide and protein quantitation
  • Accessing Distiller Quantitation Results
  • Accessing Distiller Multi-file Quantitation Results
  • Extracting quantitation results with the Distiller toolkit
  • Source code for the Shapiro-Wilk W test algorithm
  • Examples for the Mascot Parser quantitation module
• Classes for calculating masses of peptides and fragments.
  • Examples for the mass calculation module
• Accessing a Mascot Server using HTTP
  • HTTP Communication to a Mascot Server
  • Examples for the Mascot http client module