typst doc

doc/typst/chapters/a3_fundamentals-in-bottom-up-proteomics.typ

@@ -604,3 +604,22 @@ The process starts with a full scan mass spectrum from which the mass
 ]
 , caption: [The steps leading to a scored peptide #vs; mass spectrum match (PSM)]
 )<fig_xtpcpp-peptide-mass-spectrum-match-process>
+
+
+
+Once the acquisition of the experimental data is complete, the analysis of
+  these data involves going through all the fragmentation data of the
+  acquisition and performing these steps for #emph[each] MS/MS
+  spectrum (as evidenced in @fig_xtpcpp-peptide-mass-spectrum-match-process):
+
+- Get the precursor ion's #mz; value;
+- Compute the match #mz; range. For example, if the software is configured
+        with a #mz; tolerance for the #mz; matches set to 0.02 and the precursor
+        ion's #mz; value is 1254.25, then the match #mz; range would be
+        [1254.23#sym.dash.en;1254.27];
+- Construct a list of all the peptides in the database that have their
+        #mz; value contained in the match #mz; range;
+- For #emph[each] peptide in the list returned from
+        the database, compare its theoretical MS/MS spectrum with the
+        experimental one. Compute a HyperScore for comparison.
+