typst doc

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

@@ -518,5 +518,27 @@ This format is really simple, because it only contains three information
 - The protein description (#code-raw("NP_001149383 serine/threonine-protein kinase receptor")) that provides some functional data bits for the protein at hand;
 - The protein sequence (the rest of the stanza above).
 
-The first (id) and second (description) information bits are used in
-    various places in the &i2mcq; program.
+The first (id) and second (description) information bits are used in various places in the &i2mcq; program.
+
+
+The protein databases are used by the protein identification software as the
+    very first step in a bottom-up proteomics data analysis process: the
+    proteins in the database are digested #foreignphrase[in silico] in order to produce a list of peptides that retain a
+    connection to the protein from which they were generated. For each one of
+    all these peptides, the following data bits are computed (<xref
+    linkend="fig_xtpcpp-in-silico-and-real-workflows"/>, top panel):
+
+/ sequence: The peptide's sequence;
+/ #mz; value: The peptide's #mz; value, often
+          computed for the mono-protonated (&mh;) ion;
+/ MS/MS spectrum: The peptide's fragmentation
+          spectrum is nothing but an array of #mz; values corresponding to the
+          set of calculated fragments (of the b and y ion series). The #mz;
+          values of the product ions are crucial for the database search
+          algorithm;
+
+
+The next step is the establishment of a relation between the experimental
+    MS/MS data acquired by the instrument and the theoretical MS/MS spectra
+    computed from the protein sequences in the database. This next step is
+    described in detail in the next sections.