# HG changeset patch
# User bornea
# Date 1463504461 14400
# Node ID 71feabcbe3d269e68d09cafd7f3ebfe9ac454bdc
# Parent  5f09f5eeda75b7757ba3f17acc6613fbe3fa7c7d
Uploaded

diff -r 5f09f5eeda75 -r 71feabcbe3d2 nsaf_scoring.xml
--- a/nsaf_scoring.xml	Wed May 11 12:52:57 2016 -0400
+++ b/nsaf_scoring.xml	Tue May 17 13:01:01 2016 -0400
@@ -36,12 +36,16 @@
   <help>
 NSAF Scoring Table
 ^^^^^^^^^^^^^^^^^^
+This tool is a static version of the APOSTL interactive affinity proteomics analysis software that calculates the NSAF, NSAF Score, and optionally the CRAPomePCT.
 
-The NSAF score is the ratio of the NSAF for test preys versus control preys normalized by the number of controls.
-The NSAF score performs similarly to the SaintScore in spectral counting data following a sigmoidal relationship 
+The NSAF Score is the ratio of the NSAF for test preys versus control preys normalized by the number of controls.
+The NSAF Score performs similarly to the SaintScore in spectral counting data following a sigmoidal relationship 
 whereas with MS1 intensity data, NSAF scoring tracks sigmoidally to the log2 fold-change. The NSAF score is 
 designed as a less stringent alternative to the SaintScore to complement the analysis, functioning as an empirical fold-change. 
 
+CRAPomePCT is the probability of a true interaction based on the abundance of a protein in the CRAPome database.
+
+APOSTL was developed at H. Lee Moffitt Cancer Center and Research Institute and distributed under a GNU General Public License (GPL). 
 --------------
 
 **1) SAINT Output File**
@@ -59,7 +63,7 @@
 
 **3) CRAPome File**
 
-Please specify an *CRAPome* file for Bubble Graph creation. An *Inter*
+Please specify an *CRAPome* file for Bubble Graph creation. An *CRAPome*
 file should contain five columns: IP name, Mapped Gene Symbol, Number of 
 Experiments (ratio), and Average spectral counts, and Max spectral counts.