typst doc

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

@@ -476,3 +476,37 @@ In bottom-up proteomics, two different kinds of mass spectrometric data are requ
 
 - The #mz; values of the fragments (the product ions) of the peptidic precursor ion that has undergone an MS/MS gas phase fragmentation#footnote[Most often, that fragmentation step is performed using collisionally-activated dissociation (CID). In this process, the peptidic precursor ion is first isolated in the gas phase on the basis of its #mz; value and then is accelerated against a gas #quote[fog] inside of the collision cell of
           the instrument. The ion hits gas molecules multiple times, acquires a lot of energy and finally breaks.].
+          
+
+These two kinds of data are necessary because the protein identification
+    process is based on searches in protein databases using the precursion ions'
+    #mz; value and the #mz; values of that ion's fragments when it is
+    fragmented. The way the protein databases are used as the substrate of these
+    searches is described in the next section.
+
+
+=== The Protein Databases and Their Use<sect_the-protein-databases-and-their-use>
+
+The previous section ended on the idea that the protein identification
+    process, that is based on the analysis of all the peptides of a peptidic
+    mixture resulting from the endoproteolysis of a sample containing many
+    proteins, requires searches into protein databases.
+
+    
+
+A bottom-up proteomics experiment typically needs at least one protein database: a database listing all the known proteins of the organism from which the initial sample of proteins was prepared. That organism might be a bacterium, a Eucaryote, like a fungus, a protist, a plant, a mammalian#ellipsis; Optional databases might be used, like protein databases listing all known protein contaminants, for example.
+
+
+The protein databases are files in the following FASTA format:
+
+
+#code-fasta(">GRMZM2G009506_P01 NP_001149383 serine/threonine-protein kinase receptor
+MEEQHMAGPPYRYRLQHRRLMDIAPASASDDDSGHHGSNGMAIMVSILVVVIVCTLFYCV
+YCWRWRKRNAVRRAQIERLRPMSSSDLPLMDLSSIHEATNSFSKENKLGEGGFGPVYRGV
+MGGGAEIAVKRLSARSRQGAAEFRNEVELIAKLQHRNLVRLLGCCVERDEKMLVYEYLPN
+RSLDSFLFDSRKSGQLDWKTRQSIVLGIARGMLYLHEDSCLKVIHRDLKASNVLLDNRMN
+PKISDFGMAKIFEEEGNEPNTGPVVGTYGYMAPEYAMEGVFSVKSDVFSFGVLVLEILSG
+QRNGSMYLQEHQHTLIQDAWKLWNEDRAAEFMDAALAGSYPRDEAWRCFHVGLLCVQESP
+DLRPTMSSVVLMLISDQTAQQMPAPAQPPLFASSRLGRKASASDLSLAMKTETTKTQSVN
+EVSISMMEPRFWADPGTSNGAATSHPATGACKKRGGQGGDRNVKDGLAARTPTHQPVARW
+HHDRRIVD")

doc/typst/template.typ

@@ -204,6 +204,7 @@
 #let mz = "m/z"
 #let mh = [[M+H]#super[+]]
 #let mnh = [[M+nH]#super[n+]]
+#let ellipsis = "..."
 
 
 #let block-tip(body) = block(width: 100%, {
@@ -248,3 +249,14 @@ show raw.line: it => block(
   raw(code, lang: "bash")
   v(6pt)
 }
+
+
+#let code-fasta(code) = {
+
+  set align(center)
+  rect(inset: 3em, stroke: rgb("#afafaf"),fill: rgb("#f5f5f6"),{
+  set align(left)
+  set text(fill: rgb("#5c5c5d"))
+  box(raw(code, lang: "text"))
+  })
+}