Contents

== Step by step 
Guide for basic processing of mass spectrometry data derived from Bioworks 3.2.

=== Database Search Options

There are two flavors for estimating a false positive identification rate for
protein identification search engines.  The first uses two databases: one
normal, the other a decoy ({'Two-DB'}[link:files/tutorial/two_db_search.html]).  The second method ({'Cat-DB'}[link:files/tutorial/cat_db_search.html]) uses a
single databases where decoy proteins have been inserted at the bottom of the
file.  Each method has its advantages and limitations:

    Two-DB:   Pros: Database size unchanged.
                    Prophet prefers a normal database.
              Cons: No independent estimation of FPR for Bioworks and Prophet probs. 
                    Multiple parameters make it difficult to select a specfic FPR -
                      you take the FPR you get or keep re-filtering.

    Cat-DB:   Pros: Independent estimation of Bioworks and Prophet probs.
                    Can select desired FPR on single parameter (probability).
              Cons: Probabilities (and some other score functions) 
                      are influenced by presence of decoys and database size.

How to: {Two-DB Search}[link:files/tutorial/two_db_search.html] | {Cat-DB Search}[link:files/tutorial/cat_db_search.html]

Version data entries

1 entries across 1 versions & 1 rubygems

Version	Path
mspire-0.1.3	tutorial/database_searching