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Classes | Modules

Mascot results file module

Classes

class  ms_inputquery
 This class encapsulates the input data in the mascot results file. More...
class  ms_mascotresfile
 The first requirement before using any other functions or classes is to create an ms_mascotresfile object. More...
class  ms_mascotresults
 Abstract class for either ms_peptidesummary or ms_proteinsummary. More...
class  ms_mascotresults_params
 Class which provides constructor parameters for either ms_peptidesummary or ms_proteinsummary. More...
class  ms_peptide
 This class encapsulates a peptide from the mascot results file. More...
class  ms_peptidesummary
 Use this class to get peptide summary results. More...
class  ms_protein
 This class encapsulates a protein in the mascot results file. More...
class  ms_proteinsummary
class  ms_searchparams
 This class encapsulates the search parameters in the mascot results file. More...
class  ms_unigene
 This class encapsulates a complete unigene file. More...
class  ms_unigene_entry
 This class encapsulates a single entry from a unigene file. More...

Modules

 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
 Using the singleHit parameter to return a single protein
 Automated repeating of searches
 Retrieving the results of a decoy search
 Using Percolator scores
 Caching Mascot Results
 Combining multiple .dat files
 Query-level modifications
 Spectral libraries
 Spectral library score threshold (advanced reading)

Detailed Description

The Mascot results files module is used for parsing information from the results files. This data is typically used to populate a database with search results, or to provide custom reports. The standard Mascot reports uses this module.

Copyright © 2016 Matrix Science Ltd.  All Rights Reserved. Generated on Fri Jun 2 2017 01:44:51