CRAN submission protViz 0.3.1

```{sh}
 R CMD build --compact-vignettes="gs+qpdf" protViz
   --resave-data --md5
```

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: protViz
 Type: Package
 Title: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
-Version: 0.3.0
+Version: 0.3.1
 Authors@R: c(person("Christian", "Panse", email = "cp@fgcz.ethz.ch", role = c("aut", "cre"), 
         comment = c(ORCID = "0000-0003-1975-3064")),
 	person("Jonas", "Grossmann", email = "jg@fgcz.ethz.ch", role = "aut",

vignettes/protViz.Rnw

@@ -100,7 +100,7 @@ substr(F$getSequences(), 1, 60)
 {\em The currency in proteomics are the peptides.}
 In proteomics, proteins are digested to so-called peptides since peptides are much easier to handle biochemically than proteins. Proteins are very different in nature some are very sticky while others are soluble in aqueous solutions while again are only sitting in membranes. Therefore, proteins are chopped up into peptides because it is fair to assume, that for each protein, there will be many peptides behaving well so that they can be measured with the mass spectrometer. This step introduces another problem, the so-called protein inference problem. In this package here, we do not touch at all upon the protein inference.
 
-\subsection{Computing the Parent Ion Mass and Hydrophobicity of a Peptide Sequence}
+\subsection{Computing Mass and Hydrophobicity of a Peptide Sequence}
 
 \code{parentIonMass} computes the mass of an amino acid sequence.
 <<>>=

vignettes/protViz.bib

@@ -318,4 +318,30 @@ @Article{pmid15238601
 DOI={10.1074/mcp.M400031-MCP200}
 }
 
+@article{rawDiag,
+  doi = {10.1101/304485},
+  url = {https://doi.org/10.1101/304485},
+  year  = {2018},
+  month = {apr},
+  publisher = {Cold Spring Harbor Laboratory},
+  author = {Christian Trachsel and Christian Panse and Tobias Kockmann and Witold Eryk Wolski and Jonas Grossmann and Ralph Schlapbach},
+  title = {{rawDiag} - an R package supporting rational {LC}-{MS} method optimization for bottom-up proteomics}
+}
+
+@article{Egloff2018,
+  doi = {10.1101/287813},
+  url = {https://doi.org/10.1101/287813},
+  year  = {2018},
+  month = {mar},
+  publisher = {Cold Spring Harbor Laboratory},
+  author = {Pascal Egloff and Iwan Zimmermann and Fabian M. Arnold and Cedric A.J. Hutter and Damien Morger and Lennart Opitz and Lucy Poveda and Hans-Anton Keserue and Christian Panse and Bernd Roschitzki and Markus Seeger},
+  title = {Engineered Peptide Barcodes for In-Depth Analyses of Binding Protein Ensembles}
+}
 
+@misc{peakplot,
+author = {Panse, Christian and Gerrits, Bertran and Schlapbach, Ralph },
+title = {{PEAKPLOT}: {Visualizing Fragmented Peptide Mass Spectra in Proteomics}},
+url = {https://www.r-project.org/conferences/useR-2009/abstracts/pdf/Panse+Gerrits+Schlapbach.pdf},
+note = {useR!2009 conference, Rennes, F},
+year = {2009},
+}