Bjorn Victor heeft ook zijn template voor een doctoraatsthesis doorgestuurd. In zijn thesis wordt gebruik gemaakt van Tikz en PGF.
(Downloaded from LaTeX templates en logo's)
\begin
Opdag hvorfor 18 millioner mennesker verden rundt stoler på Overleaf med deres arbejde.
\documentclass[a4paper,12pt]{book} %
\usepackage[margin=2.5cm,a4paper]{geometry} %lmargin=2.5cm,rmargin=4cm,tmargin=3cm,bmargin=3cm
\usepackage{amsmath,amssymb,mathtools,lineno,graphicx,textcomp,booktabs,url,setspace,xcolor,soul,eurosym}
% \usepackage{multirow,listings,setspace,gnuplottex,latexsym,keyval,ifthen,moreverb,lscape,forest}
\usepackage{multirow,listings,setspace,latexsym,keyval,ifthen,moreverb,lscape,forest}
\graphicspath{{fig/}}
\usepackage[figuresright]{rotating}
\usepackage[]{microtype} %activate={true,nocompatibility},final,kerning=true,spacing=true,factor=1100,stretch=10,shrink=10
\usepackage{tikz,pgfplots}
\usetikzlibrary{calc,shapes,arrows,intersections,shadows}
\usepgflibrary{arrows.new}
\usetikzlibrary{arrows.new} % LATEX and plain TEX when using TikZ
\tikzset{>=latex}
\newif\ifpienumberinlegend
\pgfkeys{/number in legend/.code=
\expandafter\let\expandafter\ifpienumberinlegend
\csname if#1\endcsname
\ifpienumberinlegend
\let\legendbeforenumber\beforenumber
\let\legendafternumber\afternumber
\def\beforenumber##1\afternumber{}%
\fi,
/number in legend/.default=true
}
\usepackage{chemfig}
\usepackage[]{threeparttable}
\usepackage[indention=0.5cm,labelsep=colon,font={sf,small},labelfont={bf,sf}]{caption}
\usepackage[indention=0.5cm,font={sf,small},labelfont={bf,sf}]{subcaption}
\definecolor{light-gray}{gray}{0.90} %not always visible on a dell screen!!!
\usepackage{fancyhdr}
\pagestyle{fancy}
\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
\fancypagestyle{frontmatter}{%
\fancyhf{}
\fancyfoot[RO,LE]{\textsf{Page \thepage}}
\fancypagestyle{plain}{
\renewcommand{\headrulewidth}{0pt}
\fancyhead{}
\fancyfoot[RO,LE]{\textsf{Page \thepage}}
}
}
\fancypagestyle{mainmatter}{%
\fancyhf{}
\fancyhead[RO,LE]{\nouppercase{\small \textsf{\leftmark}}}
\fancyfoot[RO,LE]{\textsf{Page \thepage}}
}
\setlength{\headheight}{15pt}
\newcounter{letternum}
\newcounter{lettersum}
\setcounter{lettersum}{13}
\newlength{\thumbtopmargin}
\setlength{\thumbtopmargin}{1cm}
\newlength{\thumbbottommargin}
\setlength{\thumbbottommargin}{3cm}
\newlength{\thumbheight}
\pgfmathsetlength{\thumbheight}{%
(\paperheight-\thumbtopmargin-\thumbbottommargin)/\value{lettersum}}
\newlength{\thumbwidth}
\setlength{\thumbwidth}{1.5cm}
\tikzset{
thumb/.style={
% draw=black,
fill=light-gray,
text=black,
minimum height=\thumbheight, %\thumbheight,
text width=\thumbwidth,
outer sep=0pt,% outer sep=10pt,
font=\sffamily\Huge,
}
}
\newcommand{\oddthumb}[1]{%
\begin{tikzpicture}[remember picture, overlay]
\node [thumb,text centered,anchor=north east,] at ($%
(current page.north east)-%
(0,\thumbtopmargin+\value{letternum}*\thumbheight)%
$) {#1};
\end{tikzpicture}
}
\newcommand{\eventhumb}[1]{%
\begin{tikzpicture}[remember picture, overlay]
\node [thumb,text centered,anchor=north west,] at ($%
(current page.north west)-%
(0,\thumbtopmargin+\value{letternum}*\thumbheight)%
$) {#1};
\end{tikzpicture}
}
% create a new command to set a new lettergroup
\newcommand{\lettergroup}[1]{%
\fancyhead[LO]{\oddthumb{#1}}%
\fancyhead[RE]{\eventhumb{#1}}%
\fancypagestyle{chapterstart}{%
\renewcommand{\headrulewidth}{0pt}
\renewcommand{\footrulewidth}{0pt}
\fancyhf{}
\chead{\oddthumb{#1}}% chapters start only on odd pages
\fancyfoot[RO,LE]{\textsf{Page \thepage}} %\fancyfoot[RO,LE]{\textsf{Page \thepage}}
}
\thispagestyle{chapterstart}
\stepcounter{letternum}%
}
\usepackage[numbib,nottoc]{tocbibind} %numbib
%\usepackage[final]{pdfpages}
\usepackage[]{natbib} %numbers,sort&compress
\usepackage[Sonny]{fncychap} %Sonny
\usepackage[colorlinks,linkcolor=black,urlcolor=black,citecolor=black]{hyperref} %load hyperref after fncychap
\hypersetup{%
pdftitle = {A title},
pdfsubject = {A subject},
pdfkeywords = {import keywords},
pdfauthor = {Me of course},
pdfcreator = {\LaTeX\ with package \flqq hyperref\frqq},
}
\usepackage[]{cleveref} % load cleveref after hyperref
\setlength{\parindent}{0cm}
\renewcommand{\contentsname}{Table of Contents}
\renewcommand{\listfigurename}{List of Figures}
\renewcommand{\listtablename}{List of Tables}
\renewcommand{\appendixname}{}
\makeatletter
\newenvironment{chapquote}[2][2em]
{\setlength{\@tempdima}{#1}%
\def\chapquote@author{#2}%
\parshape 1 \@tempdima \dimexpr\textwidth-2\@tempdima\relax%
\itshape}
{\par\normalfont\hfill--\ \chapquote@author\hspace*{\@tempdima}\par\bigskip}
\makeatother
\setlength{\parindent}{0cm}
\pgfplotsset{compat=1.12}
%%%%%%%%%%%%%%%% BEGIN DOCUMENT %%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
\onehalfspace
\frontmatter
\pagestyle{frontmatter}
\lstset{language=Perl}
%%%%%%%%%%%%%%%% BEGIN TITLEPAGE %%%%%%%%%%%%%%%%%%
\begin{titlepage}
\centering
\includegraphics[width=\textwidth]{DI-eps-converted-to.pdf}
\vspace{1cm}
\includegraphics[width=2.25cm]{ITGlogo_new}
\vspace{2.25cm}
{\Huge \textsf{Proteomic analysis of \textit{Taenia} spp. excretion/secretion proteins: the search for \textit{Taenia solium}-specific diagnostic antigens}}
\vspace{2.25cm}
{\LARGE \textsf{Bjorn Victor}}
\vspace{2.25cm}
{\textsf{Proefschrift voorgedragen tot het behalen van de graad van \\Doctor in de Diergeneeskundige Wetenschappen, 2014}}
\vfill
{\textsf{Promotoren: \\
Prof. Dr. Pierre Dorny\\Dr. Sarah Gabri\"el\\ Dr. Magnus Palmblad}}
\vfill
{\textsf{Vakgroep Virologie, Parasitologie en Immunologie\\
Faculteit Diergeneeskunde, Universiteit Gent \\
Salisburylaan 133, B-9820 Merelbeke}}
\end{titlepage}
%%%%%%%%%%%%%%%% END TITLEPAGE %%%%%%%%%%%%%%%%%%
\newpage{\thispagestyle{empty}\cleardoublepage}
\thispagestyle{empty}
\phantom{text}
\vfill
\begin{chapquote}{Douglas Adams, \textit{The Long Dark Tea-Time of the Soul} (1988).}
``I may not have gone where I intended to go, but I think I have ended up where I needed to be.''\\
\end{chapquote}
\vfill
\newpage{\thispagestyle{empty}\cleardoublepage}
\chapter{Acknowledgements}
text
\newpage{\thispagestyle{empty}\cleardoublepage}
%%%%%%%%%%%%%%%% BEGIN LISTS %%%%%%%%%%%%%%%%%%%%%%%
\newpage{\thispagestyle{empty}\cleardoublepage}
\tableofcontents
\newpage{\thispagestyle{empty}\cleardoublepage}
\listoffigures
\newpage{\thispagestyle{empty}\cleardoublepage}
\listoftables
\newpage{\thispagestyle{empty}\cleardoublepage}
%%%%%%%%%%%%%%%% END LISTS %%%%%%%%%%%%%%%%%%%%%%%
\mainmatter
%\linenumbers %this will destroy the red frame around the protein info!!!
%%%%%%%%%%%%%%%%%%%%%%% General introduction %%%%%%%%%%%%%%%%
\newpage{\thispagestyle{empty}\cleardoublepage}
\pagestyle{mainmatter}
\chapter{General Introduction} \label{chap:generalintro}
\lettergroup{\thechapter}
text
%%%%%%%%%%%%%%%%%%%%%%% T. solium literature %%%%%%%%%%%%%%%%
%
\newpage{\thispagestyle{empty}\cleardoublepage}
\chapter{\textit{Taenia solium}: An Introduction} \label{chap:tsolliterature}
\lettergroup{\thechapter}
\section{\textit{Taenia solium} taeniasis and cysticercosis}
\textit{Taenia solium} is a tapeworm belonging to the Taeniidae family (\Cref{fig:taxo}).
\begin{sidewaysfigure}
\resizebox{1\linewidth}{!}{
\centering
\begin{forest}
[Kingdom [Phylum [Class [Order [Family [Genus\textit{\phantom{j}}]]]]]]
\end{forest}
\quad
\begin{forest}
[Metazoa
[Platyhelminthes
[Cestoda [Cyclophyllidea [Taeniidae [\textbf{\textit{Taenia}}][\textit{Echinococcus}]][Hymenolepididae[\textit{Hymenolepis}]]] ]
[Trematoda [Strigeidida[Schistosomatidae[\textit{Schistosoma}]]] [Opisthorchiida[Opisthorchiidae[\textit{Clonorchis}]]]]
]
[Nematoda
[Enoplea[Trichocephalida[Trichinellidae[\textit{Trichinella}]][Trichuridae[\textit{Trichuris}]]] ]
[Chromadorea [Ascaridida[Ascarididae[\textit{Ascaris}]]][Rhabditida[Strongylidae[\textit{Strongylus}]][Rhabditidae[\textit{Caenorhabditis}]]] ]
]
]
\end{forest}
}
\caption{text}
\label{fig:taxo}
\end{sidewaysfigure}
The adult stage of the worm \citep{Linne:1758uq} develops in the upper third section of the small intestine of humans, %which is the duodenum-jejunum
the only final host, where it causes an infection called taeniasis (\Cref{fig:lifecycle}).
\begin{figure}[!htbp]
\centering
{\sffamily
\begin{tikzpicture}
\tikzstyle{every node}=[anchor=center]
\tikzstyle{column 3}=[text width=4cm,text height=2.3cm,text centered]
\tikzstyle{column 2}=[text width=5cm,text centered]
\tikzstyle{column 1}=[text width=4cm,text height=1.6cm,text centered]
\matrix [row sep=-0.30cm,column sep=1cm] %draw
{
\node(v0)[text height=0.6cm]{\large\underline{Intermediate host}}; & &\node(v0)[text height=0.6cm]{\large\underline{Final host}}; \\
& \node(v2)[]{\scalebox{0.15}{ %0.6
\begin{tikzpicture}[line width=1mm] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (15,10);
\draw [blue] (1,7) to [out=10,in=170] (14,7);
\draw [blue] (1,6) to [out=10,in=170] (14,6);
\draw [blue] (1,5) to [out=10,in=185] (5.9,5.65);
\draw [blue] (9.1,5.65) to [out=-5,in=170] (14,5);
\draw [blue] (1,4) to [out=10,in=185] (5,4.6);
\draw [blue] (10,4.6) to [out=-5,in=170] (14,4);
\draw [blue] (1,3) to [out=10,in=185] (5.5,3.6);
\draw [blue] (9.5,3.6) to [out=-5,in=170] (14,3);
\draw [blue] (1,2) to [out=10,in=170] (14,2);
\draw [blue] (1,1) to [out=10,in=170] (14,1);
\draw [blue,] (7.5,4.5) circle [radius=0.3];
\draw [blue] (7.2,4.55) to [out=75,in=-45] (7,5.96) ;
\draw [blue] (7.8,4.45) to [out=75,in=-65] (8,5.96) ;
\draw [blue,thick] (7.4,4.4) circle [radius=0.05];
\draw [blue,thick] (7.6,4.6) circle [radius=0.05];
\draw [blue,thick] (7.6,4.4) circle [radius=0.05];
\draw [blue,thick] (7.4,4.6) circle [radius=0.05];
\draw [blue] (7.5,4.5) ellipse (2.5cm and 1.5cm);
\end{tikzpicture}}\\Consumption of raw or undercooked infected pork}; &\\
\node(v6){\scalebox{0.15}{ %0.6
\begin{tikzpicture}[line width=1mm] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (15,10);
\draw [blue] (13,0) -- (13,5) to [out=90,in=0] (10,8) -- (5,8);% to [out=0,in=105] (8.75,0) -- (6.25,0);
\draw[blue] (13,0) -- (12.5,0.5) -- (12,0) -- (12,3) to [out=90,in=90] (11,3) -- (11,0) -- (10.5,0.5) -- (10,0) -- (10,3) to [out=210,in=330] (5,3) -- (5,0) -- (4.5,0.5) -- (4,0) -- (4,3) to [out=90,in=90] (3,3) -- (3,0) -- (2.5,0.5) -- (2,0) -- (2,5);
\draw [blue] (3,7) circle [radius=2.25]; %kop
\draw [blue] (3,6) circle [radius=0.75]; %neus
\draw [blue] (2.7,6) circle [radius=0.1];
\draw [blue] (3.30,6) circle [radius=0.1];
\draw [blue] (2,7.5) circle [radius=0.15]; %ogen
%\draw [blue,fill=blue] (2,7.45) circle [radius=0.07];
\draw [blue] (4,7.5) circle [radius=0.15]; %ogen
%\draw [blue,fill=blue] (4,7.45) circle [radius=0.07];
\draw [blue] (14,9) -- (12.11,7.11); %staart
\draw [blue] (12.7,8.35) circle [radius=0.45];
\draw [blue] (1,8) to [out=135,in=270] (0.5,9.5) to [out=0,in=135] (2,9) ;
\draw [blue] (4,9) to [out=45,in=180] (5.5,9.5) to [out=-90,in=45] (5,8) ;
\draw [blue] (17.5,5.5) ellipse (2cm and 1cm);
\draw [blue,] (17.5,5.5) circle [radius=0.3];
\draw [blue] (17.2,5.55) to [out=75,in=-45] (17,6.45) ;
\draw [blue] (17.8,5.45) to [out=75,in=-65] (18,6.45) ;
\draw [blue,thick] (17.4,5.4) circle [radius=0.05];
\draw [blue,thick] (17.6,5.6) circle [radius=0.05];
\draw [blue,thick] (17.6,5.4) circle [radius=0.05];
\draw [blue,thick] (17.4,5.6) circle [radius=0.05];
\end{tikzpicture}}\\Porcine cysticercosis};& &
\node(v4)[]{\scalebox{0.18}{ %0.6
\begin{tikzpicture}[line width=1mm] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (15,15);
\draw [blue] (7.65,5) -- (7.65,1) to [out=270,in=180] (8.525,0) to [out=0,in=270] (9.4,1) -- (9.4,8) -- (9.5,8) -- (9.5,5) to [out=270,in=180] (10,4.5) to [out=0,in=270] (10.5,5) -- (10.5,9) to [out=90,in=0] (9.5,10) -- (5.5,10) to [out=180,in=90] (4.5,9) -- (4.5,5) to [out=270,in=180] (5,4.5) to [out=0,in=270] (5.5,5) -- (5.5,8) -- (5.6,8) -- (5.6,1) to [out=270,in=180] (6.475,0) to [out=0,in=270] (7.35,1) -- (7.35,5) -- (7.65,5);
\draw [blue] (7.5,11.8) circle [radius=1.3];
\draw [blue] (2,8) circle [radius=0.4];
\draw [blue,thick] (2.15,8.15) circle [radius=0.05];
\draw [blue,thick] (2.15,7.85) circle [radius=0.05];
\draw [blue,thick] (1.85,8.15) circle [radius=0.05];
\draw [blue,thick] (1.85,7.85) circle [radius=0.05];
\draw [blue] (2.2,7.65) to [out=-75,in=75] (2.2,4.6) ;
\draw [blue] (1.8,7.65) to [out=-75,in=75] (1.8,4.6) ;
\draw [blue] (2.2,4.6) to [out=-105,in=105] (2.2,2) ;
\draw [blue] (1.8,4.6) to [out=-105,in=105] (1.8,2) ;
\draw [blue] (1.95,7) -- (2.35,7) ;
\draw [blue] (2.05,6) -- (2.45,6) ;
\draw [blue] (1.9,5) -- (2.3,5) ;
\draw [blue] (1.65,4) -- (2.05,4) ;
\draw [blue] (1.6,3) -- (2,3) ;
\end{tikzpicture}}\\Human taeniasis}; \\
& \node(v8)[]{\scalebox{0.1}{ %0.6
\begin{tikzpicture}[line width=1mm] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (15,10);
\draw [blue] (7.5,5) circle [radius=2.5];
\draw [blue] (7.5,5) circle [radius=1.8];
\draw [blue] (7.35,5) to [out=90,in=-45] (7,6) ;
\draw [blue] (7.65,5) to [out=90,in=-45] (7.4,6) ;
\draw [blue] (7,4.5) to [out=135,in=0] (6.25,5) ;
\draw [blue] (7.3,4.6) to [out=135,in=0] (6.5,5.2) ;
\draw [blue] (7.7,4.6) to [out=45,in=180] (8.25,5.2) ;
\draw [blue] (8.,4.5) to [out=45,in=180] (8.5,5) ;
\end{tikzpicture}}\\Eggs ingested by pigs\\ (coprophagy or accidental)}; &\\
\node(v12){\scalebox{0.18}{ %0.6
\begin{tikzpicture}[line width=1mm] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (15,15);
\draw [blue] (7.65,5) -- (7.65,1) to [out=270,in=180] (8.525,0) to [out=0,in=270] (9.4,1) -- (9.4,8) -- (9.5,8) -- (9.5,5) to [out=270,in=180] (10,4.5) to [out=0,in=270] (10.5,5) -- (10.5,9) to [out=90,in=0] (9.5,10) -- (5.5,10) to [out=180,in=90] (4.5,9) -- (4.5,5) to [out=270,in=180] (5,4.5) to [out=0,in=270] (5.5,5) -- (5.5,8) -- (5.6,8) -- (5.6,1) to [out=270,in=180] (6.475,0) to [out=0,in=270] (7.35,1) -- (7.35,5) -- (7.65,5);
\draw [blue] (7.5,11.8) circle [radius=1.3];
\draw [blue] (15.5,5.5) ellipse (1.7cm and 0.9cm);
\draw [blue,] (15.5,5.5) circle [radius=0.3];
\draw [blue] (15.2,5.55) to [out=75,in=-45] (15,6.35) ;
\draw [blue] (15.8,5.45) to [out=75,in=-65] (16,6.35) ;
\draw [blue,thick] (15.4,5.4) circle [radius=0.05];
\draw [blue,thick] (15.6,5.6) circle [radius=0.05];
\draw [blue,thick] (15.6,5.4) circle [radius=0.05];
\draw [blue,thick] (15.4,5.6) circle [radius=0.05];
\end{tikzpicture}}\\Human (neuro) cysticercosis}; & \node(v11){\scalebox{0.1}{ %0.6
\begin{tikzpicture}[line width=1mm] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (15,10);
\draw [blue] (7.5,5) circle [radius=2.5];
\draw [blue] (7.5,5) circle [radius=1.8];
\draw [blue] (7.35,5) to [out=90,in=-45] (7,6) ;
\draw [blue] (7.65,5) to [out=90,in=-45] (7.4,6) ;
\draw [blue] (7,4.5) to [out=135,in=0] (6.25,5) ;
\draw [blue] (7.3,4.6) to [out=135,in=0] (6.5,5.2) ;
\draw [blue] (7.7,4.6) to [out=45,in=180] (8.25,5.2) ;
\draw [blue] (8.,4.5) to [out=45,in=180] (8.5,5) ;
\end{tikzpicture}}\\Eggs (accidentally) ingested by humans}; &\\
};
%\draw [->] (v2.west) -- (v4.north) node [above,text centered,midway] {replacement};
\draw [-latex new, arrow head=2mm] [blue,thick] (v2.east) -- (v4.north);
%\draw [arrows=->] [blue,thick] (v1.south) -- (v4.north);
\draw [-latex new, arrow head=2mm] [blue,thick] (v4.south) -- (v8.east);
\draw [-latex new, arrow head=2mm] [blue,thick] (v4.south) -- (v11.east) node [right,blue,midway,text width=2.8cm,text height=1.2cm] {\textcolor{black}{Proglottids/eggs \\shed with stools}};
%\draw [arrows=->] [blue,thick] (v9.north) -- (v6.south);
\draw [-latex new, arrow head=2mm] [blue,thick] (v8.west) -- (v6.south);
\draw [-latex new, arrow head=2mm] [blue,thick] (v11.west) -- (v12.east);
\draw [-latex new, arrow head=2mm] [blue,thick] (v6.north) -- (v2.west);
\end{tikzpicture}}
\caption{text}
\label{fig:lifecycle}
\end{figure}
%%%%%%%%%%%%%%%%%% The Hitchhiker's Guide to Proteomics %%%%%%%%%%%%%%%%
\newpage{\thispagestyle{empty}\cleardoublepage}
\chapter[The Hitchhiker's Guide to Proteomics]{The Hitchhiker's Guide to Proteomics\protect\footnote{Title adapted from the novel ``The Hitchhiker's Guide to the Galaxy'', written by Douglas Adams and published by Pan Books in 1979.}}\label{chap:proteomics}
\lettergroup{\thechapter}
\begin{figure}[!htbp]
\centering
{\sffamily
\begin{tikzpicture}
\tikzstyle{every node}=[anchor=center]
\tikzstyle{column 1}=[text width=2.5cm,text centered]
\tikzstyle{column 2}=[text width=3cm,text centered]
\tikzstyle{column 3}=[text width=3cm,text centered]
\tikzstyle{column 4}=[text width=3cm,text centered]
\matrix [row sep=0.25cm,column sep=1cm] %draw,
{
\node(v1)[]{genomics}; & \node(v2)[]{transcriptomics};& \node(v3)[]{PROTEOMICS}; &\node(v4)[]{metabolomics};\\
\node(v5)[]{what can happen}; & \node(v6)[]{what will \\happen}; & \node(v7)[]{what is happening}; &\node(v8)[]{what has happened};\\
};
\draw [-latex new, arrow head=3mm] [thick] (v1.east) -- (v2.west);
\draw [-latex new, arrow head=3mm] [thick] (v2.east) -- (v3.west);
\draw [-latex new, arrow head=3mm] [thick] (v3.east) -- (v4.west);
\draw [arrows=-] [thick,dotted] (v1.south) -- (v5.north);
\draw [arrows=-] [thick,dotted] (v2.south) -- (v6.north);
\draw [arrows=-] [thick,dotted] (v3.south) -- (v7.north);
\draw [arrows=-] [thick,dotted] (v4.south) -- (v8.north);
\end{tikzpicture}}
\caption{text}
\label{fig:proteomics}
\end{figure}
\begin{figure}[!htbp]
\centering
\subcaptionbox{IEF. \label{fig:IEF}}[.35\linewidth]{\scalebox{0.65}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (15,4);
\draw [black] (-3,2.25) -- (4,2.25) -- (4,1.75) -- (-3,1.75) -- (-3,2.25);
\draw [black] (-2,2.25) -- (-2,1.75);
\draw [black] (-1,2.25) -- (-1,1.75);
\draw [black] (-1.35,2.25) -- (-1.35,1.75);
\draw [black] (0,2.25) -- (0,1.75);
\draw [black] (0.15,2.25) -- (0.15,1.75);
\draw [black] (0.3,2.25) -- (0.3,1.75);
\draw [black] (1,2.25) -- (1,1.75);
\draw [black] (2,2.25) -- (2,1.75);
\draw [black] (2.2,2.25) -- (2.2,1.75);
\draw [black] (3,2.25) -- (3,1.75);
\draw [black] (3.3,2.25) -- (3.3,1.75);
\draw [black] (3.4,2.25) -- (3.4,1.75);
\draw [black] (3.6,2.25) -- (3.6,1.75);
\node[anchor=south,black,rotate=0] at (-2.5,2.4) {\Large \sffamily Low pH};
\node[anchor=south,black,rotate=0] at (-3,0.6) {\Large \sffamily (+)};
\draw [-latex new, arrow head=3mm,black] (-2.3,1) -- (0,1);
\draw [-latex new, arrow head=3mm,black] (3.3,1) -- (1,1);
\node[anchor=south,black,rotate=0] at (0.5,0.6) {\Large \sffamily pI};
\node[anchor=south,black,rotate=0] at (3.5,2.4) {\Large \sffamily High pH};
\node[anchor=south,black,rotate=0] at (4,0.6) {\Large \sffamily ($-$)};
\node[black,rotate=0] at (2.5,0.2) {\Large \sffamily \phantom{aa}};
\end{tikzpicture}}}\hfill
\subcaptionbox{1D-PAGE. \label{fig:1-Delectr}}[.3\linewidth]{\scalebox{0.65}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (15,4);
\draw [black] (7,0) -- (7,4) -- (7.5,4) -- (7.5,3.5) -- (8,3.5 ) -- (8,4) -- (8.5,4) -- (8.5,3.5) -- (9,3.5) -- (9,4) -- (9.5,4) -- (9.5,3.5) -- (10,3.5) -- (10,4) -- (10.5,4) -- (10.5,3.5) -- (11,3.5) -- (11,4) -- (11.5,4) -- (11.5,3.5) -- (12,3.5) -- (12,4) -- (12.5,4) -- (12.5,0) -- (7,0);
\draw [thick,black] (7.5,2.2) -- (8,2.2);
\draw [thick,black] (7.5,1.5) -- (8,1.5);
\draw [thick,black] (7.5,0.75) -- (8,0.75);
\draw [thick,black] (8.5,3) -- (9,3);
\draw [thick,black] (8.5,2) -- (9,2);
\draw [thick,black] (8.5,1) -- (9,1);
\draw [thick,black] (9.5,2.5) -- (10,2.5);
\draw [thick,black] (9.5,2.8) -- (10,2.8);
\draw [thick,black] (9.5,1.5) -- (10,1.5);
\draw [thick,black] (10.5,2.7) -- (11,2.7);
\draw [thick,black] (10.5,1.8) -- (11,1.8);
\draw [thick,black] (10.5,0.5) -- (11,0.5);
\draw [thick,black] (11.5,3) -- (12,3);
\draw [thick,black] (11.5,1.5) -- (12,1.5);
\draw [thick,black] (11.5,0.75) -- (12,0.75);
\node[anchor=south,black,rotate=0] at (13.25,3) {\Large \sffamily ($-$)};
\node[anchor=south,black,rotate=0] at (13.25,0) {\Large \sffamily (+)};
\draw [-latex new, arrow head=3mm,black] (13.25,3) -- (13.25,1) node [above,black,midway,rotate=90] {\Large \sffamily size};
%\draw [-latex new, arrow head=3mm] [thick] (7,0) -- (8,0) node [above,black,midway] {pH$\uparrow$};
\end{tikzpicture}}}\hfill
\subcaptionbox{2D-PAGE. \label{fig:2-Delectr}}[.3\linewidth]{\scalebox{0.65}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (15,4);
\draw [black] (15,0) -- (15,4) -- (15.5,4) -- (15.5,3.5) -- (21,3.5) -- (21,4) -- (21.5,4) -- (21.5,0) -- (15,0);
\draw [black,fill=black] (16, 0.75) circle [radius=0.05];
\draw [black,fill=black] (16.25, 0.75) circle [radius=0.05];
\draw [black,fill=black] (16.5, 0.75) circle [radius=0.05];
\draw [black,fill=black] (18, 1.5) circle [radius=0.05];
\draw [black,fill=black] (18, 1.75) circle [radius=0.05];
\draw [black,fill=black] (20.5, 2.5) circle [radius=0.05];
\draw [black,fill=black] (17, 2.3) circle [radius=0.05];
\draw [black,fill=black] (17.5, 0.75) circle [radius=0.05];
\draw [black,fill=black] (20, 1) circle [radius=0.05];
\draw [black,fill=black] (19.5, 1.75) circle [radius=0.05];
\draw [black,fill=black] (19, 2.8) circle [radius=0.05];
\draw [black,fill=black] (18.4, 1) circle [radius=0.05];
\draw [black,fill=black] (16.125, 2.4) circle [radius=0.05];
\draw [-latex new, arrow head=3mm,black] (16,3.85) -- (17.75,3.85);
\draw [-latex new, arrow head=3mm,black] (20.5,3.85) -- (18.75,3.85);
\node[anchor=south,black,rotate=0] at (18.25,3.45) {\Large \sffamily pI};
%\node[anchor=south,black,rotate=0] at (1,0.6) {\Large \sffamily pI};
%\draw [arrows=->,black] (4,3) -- (1.5,3);
%\node[anchor=south,black,rotate=0] at (1,0.6) {\Large \sffamily pI};
%\node[anchor=south,black,rotate=0] at (22.25,3) {\Large \sffamily ($-$)};
%\node[anchor=south,black,rotate=0] at (22.25,0) {\Large \sffamily (+)};
%\draw [-latex new, arrow head=3mm,black] (22.25,3) -- (22.25,1);
\draw [-latex new, arrow head=3mm,black] (21,3) -- (21,0.5) node [above,black,midway,rotate=90] {\Large \sffamily size};
\end{tikzpicture}}} \caption{text}
\end{figure}%
\begin{figure}[!htbp]
\centering
\scalebox{0.65}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (20,10);
\draw [black] (2,-0.9) -- (2,6.9) -- (1.7,6.9) -- (1.7,-0.9) -- (2,-0.9);
\draw [black] (1.7,-0.9) -- (2,-0.6);
\draw [black] (1.7,-0.6) -- (2,-0.3);
\draw [black] (1.7,-0.3) -- (2,0);
\draw [black] (1.7,0) -- (2,0.3);
\draw [black] (1.7,0.3) -- (2,0.6);
\draw [black] (1.7,0.6) -- (2,0.9);
\draw [black] (1.7,0.9) -- (2,1.2);
\draw [black] (1.7,1.2) -- (2,1.5);
\draw [black] (1.7,1.5) -- (2,1.8);
\draw [black] (1.7,1.8) -- (2,2.1);
\draw [black] (1.7,2.1) -- (2,2.4);
\draw [black] (1.7,2.4) -- (2,2.7);
\draw [black] (1.7,2.7) -- (2,3);
\draw [black] (1.7,3) -- (2,3.3);
\draw [black] (1.7,3.3) -- (2,3.6);
\draw [black] (1.7,3.6) -- (2,3.9);
\draw [black] (1.7,3.9) -- (2,4.2);
\draw [black] (1.7,4.2) -- (2,4.5);
\draw [black] (1.7,4.5) -- (2,4.8);
\draw [black] (1.7,4.8) -- (2,5.1);
\draw [black] (1.7,5.1) -- (2,5.4);
\draw [black] (1.7,5.4) -- (2,5.7);
\draw [black] (1.7,5.7) -- (2,6);
\draw [black] (1.7,6) -- (2,6.3);
\draw [black] (1.7,6.3) -- (2,6.6);
\draw [black] (1.7,6.6) -- (2,6.9);
\draw [black] (2,0.5) to [out=30,in=-90] (3,2.5);
\draw [black] (3,2.5) -- (2.75,2.25) -- (2.5,2.75) -- (2.1,2.5) -- (2.35,3) -- (2.1,3.5) -- (2.5,3.25) -- (2.75,3.75) -- (3,3.5);
\draw [black] (2,5.5) to [out=-30,in=90] (3,3.5);
\draw [black,fill=black] (2.25,1.5) circle [radius=0.075];
\draw [black,fill=black] (2.5,2) circle [radius=0.075];
\draw [black,fill=black] (2.3,2.25) circle [radius=0.075];
\draw [black,fill=black] (2.2,4) circle [radius=0.075];
\draw [black,fill=black] (2.75,4.25) circle [radius=0.075];
\draw [black,fill=black] (2.35,4.75) circle [radius=0.075];
\draw [black,fill=black] (5.2,3.75) circle [radius=0.075];
\draw [black,fill=black] (6.4,2.3) circle [radius=0.075];
\draw [black,fill=black] (4.8,3) circle [radius=0.075];
\draw [black,fill=black] (4,2.5) circle [radius=0.075];
\draw [black,fill=black] (6.75,3.5) circle [radius=0.075];
\draw [black,fill=black] (6,3) circle [radius=0.075];
\draw [black,fill=black] (5.4,2.5) circle [radius=0.075];
\draw [black,ultra thick,rotate=30] (3.75,1.35) -- (10,1.35) -- (10,1.60) -- (12,1.60) -- (12,1.1) -- (10,1.1) -- (10,1.35) ;
\node[black,rotate=0] at (5,7) {\Large \sffamily laser beam};
\draw [black,dotted] (6,6.5) -- (7,5.6);
\draw [black,-latex new, arrow head=3mm] (3,3) -- (4,3);
\node[black,rotate=0] at (3,-0.5) {\Large \sffamily matrix/analyte mixture};
\draw [black,dotted] (4,0) -- (2.6,1.75);
\node[black,rotate=0] at (-1,7) {\Large \sffamily target};
\node[black,rotate=0] at (-1,6.26) {\Large \sffamily plate};
\draw [black,dotted] (1,6.5) -- (1.7,5.75);
\draw [black,-latex new, arrow head=3mm] (10.5,3) -- (11.5,3);
\node[black,rotate=0] at (11.75,3) {\Large \sffamily to mass spectrometer};
\node[black,rotate=0] at (7,1.75) {\Large \sffamily charged};
\node[black,rotate=0] at (7,1) {\Large \sffamily analytes};
\draw [black,dotted] (8,2.25) -- (6.5,3);
\node[black,rotate=0] at (12,7) {\Large \sffamily focussing lenses};
\draw [black,dotted] (13,6.5) -- (11,5);
\draw [black] (10,0) -- (10,2.5) (10,3.5) -- (10,6);
\draw [black] (10.5,0) -- (10.5,2.5) (10.5,3.5) -- (10.5,6);
\draw [black] (11,0) -- (11,2.5) (11,3.5) -- (11,6);
\end{tikzpicture}}
\caption{text}
\label{fig:MALDI}
\end{figure}
\begin{figure}[!htbp]
\centering
\scalebox{0.65}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (20,20);
\node[black,rotate=0] at (9,12) {\Large \sffamily flow of liquid analytes (from the RPLC)};
\draw [black,dotted] (8.75,12) -- (5.75,12);
\draw[rotate around={-60:(12,3)},black] (0,2.4) -- (4,2.4) -- (4,1.6) -- (0,1.6) (4,2.4) -- (5,2) to [out=0,in=205] (10,3.3) (4,1.6) -- (5,2) to [out=0,in=155] (10,0.7) ;
\draw [rotate around={-60:(12,3)},black,-latex new, arrow head=3mm] (0.5,2) -- (1.5,2);
\draw [rotate around={-60:(12,3)},black,dashed,-latex new, arrow head=3mm] (3,2.75) -- (4,2.75);
\draw [rotate around={-60:(12,3)},black,dashed,-latex new, arrow head=3mm] (1.5,1.25) -- (2.5,1.25);
\draw[rotate around={-60:(12,3)},black,fill=black] (8,2) circle [radius=0.2] (9.75,2) circle [radius=0.1] (9.45,2.2) circle [radius=0.1] (9.5,1.8) circle [radius=0.1] (11,2) circle [radius=0.05] (11.2,2.2) circle [radius=0.05] (11.4,1.8) circle [radius=0.05] (11.6,2) circle [radius=0.05] (11.8,2.5) circle [radius=0.05] (11.7,1.5) circle [radius=0.05] (11.9,1.7) circle [radius=0.05] (11.5,2.3) circle [radius=0.05] (12,2) circle [radius=0.05];
\draw [black] (13,2.8) -- (14,2.8) -- (14,4) (14.5,2.5) -- (18,2.5);
\draw [black] (13,1.2) -- (14,1.2) -- (14,0) (14.5,1.5) -- (18,1.5);
\node[black,rotate=0] at (15,3.5) {\Large \sffamily drying gas (N$_{\mathsf{2}}$)};
\draw [black,dashed,-latex new, arrow head=3mm] (15,3) to [out=-140,in=0] (13.5,2.5);
\draw [black,dashed,-latex new, arrow head=3mm] (15,1) to [out=140,in=0] (13.5,1.5);
\draw [black,-latex new, arrow head=3mm] (12.5,2) -- (14.5,2);
\node[black,rotate=0] at (15,2) {\Large \sffamily to mass spectrometer };
\node[black,rotate=0] at (6,0) {\Large \sffamily $+$ $-$};
\draw [black] (6.375,0.3) -- (6.375,9.95);
\draw [black] (7,0.3) -- (7,0.5) -- (13.5,0.5) -- (13.5,1.2);
\node[black,rotate=0] at (9,11) {\Large \sffamily conducting needle};
\draw [black,dotted] (8.75,11) -- (6.7,11);
\node[black,rotate=0] at (9,10) {\Large \sffamily nebuliser gas (N$_{\mathsf{2}}$)};
\draw [black,dotted] (8.75,10) -- (7.6,10);
\node[black,rotate=0] at (9,9) {\Large \sffamily Taylor cone};
\draw [black,dotted] (8.75,9) -- (7.6,9);
\node[black,rotate=0] at (13,5) {\Large \sffamily spray of droplets};
\draw [black,dotted] (12.75,4.90) -- (10.5,4);
\end{tikzpicture}}
\caption{text}
\label{fig:ESI}
\end{figure}
\begin{figure}[!htbp]
\centering
\scalebox{0.65}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (-2,0) grid (20,4);
\draw [black] (-1.9,3.9) -- (-0.2,2.1);
\draw [black] (-2,3.8) -- (-0.3,2);
\draw [black,-latex new, arrow head=3mm] (0.25,2) -- (1.25,2);
\node[black,rotate=0] at (-2,0.5) {\Large \sffamily ESI needle};
\draw [black,dotted] (-1.5,1) -- (-0.6,2.25);
\draw [black] (9,0) -- (9.5,0) to [out=45,in=270] (10.25,1.9) -- (9,1.9) -- (9,0);
\draw [black] (9,4) -- (9.5,4) to [out=-45,in=90] (10.25,2.1) -- (9,2.1) -- (9,4);
\draw [black] (10.25,0) to [out=75,in=180] (11.5,1.5) to [out=0,in=105] (12.75,0) -- (10.25,0);
\draw [black] (10.25,4) to [out=-75,in=180] (11.5,2.5) to [out=0,in=-105] (12.75,4) -- (10.25,4);
\draw [black] (14,0) -- (13.5,0) to [out=135,in=270] (12.75,1.9) -- (14,1.9) -- (14,0);
\draw [black] (14,4) -- (13.5,4) to [out=225,in=90] (12.75,2.1) -- (14,2.1) -- (14,4);
\draw [black] (2,0) -- (2,1.5);
\draw [black] (2,4) -- (2,2.5);
\draw [black] (1.5,1.5) -- (2,1.5);
\draw [black] (1.5,2.5) -- (2,2.5);
\node[black,rotate=0] at (2.7,2.5) {\Large \sffamily ion guide};
%\draw [black,dotted] (4.8,2.75) -- (5.3,3);
%\draw [black,dotted] (5.1,2.75) -- (6,1);
\draw [black] (3,0) -- (3,0.1);
\draw [black] (3.5,0) -- (3.5,0.25);
\draw [black] (4,0) -- (4,0.5);
\draw [black] (4.5,0) -- (4.5,0.75);
\draw [black] (5,0) -- (5,1);
\draw [black] (5.5,0) -- (5.5,1.25);
\draw [black] (6,0) -- (6,1.5);
\draw [black] (6.5,0) -- (6.5,1.75);
\draw [black] (7,0) -- (7,1.9);
\draw [black] (7.5,0) -- (7.5,1.9);
\draw [black] (8,0) -- (8,1.9);
\draw [black] (3,4) -- (3,3.9);
\draw [black] (3.5,4) -- (3.5,3.75);
\draw [black] (4,4) -- (4,3.5);
\draw [black] (4.5,4) -- (4.5,3.25);
\draw [black] (5,4) -- (5,3);
\draw [black] (5.5,4) -- (5.5,2.75);
\draw [black] (6,4) -- (6,2.5);
\draw [black] (6.5,4) -- (6.5,2.25);
\draw [black] (7,4) -- (7,2.1);
\draw [black] (7.5,4) -- (7.5,2.1);
\draw [black] (8,4) -- (8,2.1);
\node[black,rotate=0] at (15.5,2.3) {\Large \sffamily ions are sequentially};
\node[black,rotate=0] at (15.5,1.7) {\Large \sffamily ejected from the trap};
%\draw [black,arrows=->] (8,2) -- (9,2);
\draw [black,-latex new, arrow head=3mm] (14,2) -- (15.2,2);
\node[black,rotate=0] at (15,0.5) {\Large \sffamily end caps};
\draw [black,dotted] (14.7,0.45) -- (9.5,1.5);
\draw [black,dotted] (14.7,0.45) -- (13.5,1.5);
\node[black,rotate=0] at (15,3.5) {\Large \sffamily ring electrode};
\draw [black,dotted] (14.7,3.5) -- (11.5,3.5);
\draw [black,fill=black] (12,2) circle [radius=0.08];
\draw [black,fill=black] (11,2) circle [radius=0.08];
\draw [black,fill=black] (11.5,2.2) circle [radius=0.08];
\draw [black,fill=black] (11.7,1.8) circle [radius=0.08];
\draw [black,fill=black] (11.3,1.9) circle [radius=0.08];
\end{tikzpicture}}
\caption{text}
\label{fig:iontrap}
\end{figure}
\begin{figure}[!htbp]
\centering
\renewcommand*\printatom[1]{\ensuremath{\mathsf{#1}}}
\scalebox{1}{
\begin{tikzpicture}
%\draw[help lines] (0,0) grid (5,2);
\node [] at (0,0) {\setatomsep{0.8cm}\chemfig[black]{H_{2}N-[:0]C(-[:-90]R_{1})(-[:90]H)-[:0]C(=[:90]O)-[:0]NH-[:0]C(-[:-90]R_{2})(-[:90]H)-[:0]C(=[:90]O)-[:0]NH-[:0]C(-[:-90]R_{3})(-[:90]H)(-[:90]H)-[:0]C(=[:90]O)-[:0]NH-[:0]C(-[:-90]R_{4})(-[:90]H)-[:0]C(=[:30]O)-[:-30]OH}};
\draw [arrows=-] [black,thick,dotted] (-3.75,1.4) -- (-3.9,1.4) -- (-3.9,-1.4) -- (-4.05,-1.4);
\draw [arrows=-] [black,thick,dotted] (-2.95,1.4) -- (-3.1,1.4) -- (-3.1,-1.4) -- (-3.25,-1.4) ;
\draw [arrows=-] [black,thick,dotted] (-1.85,1.4) -- (-2,1.4) -- (-2,-1.4) -- (-2.15,-1.4) ;
\draw [arrows=-] [black,thick,dotted] (-1.05,1.4) -- (-1.2,1.4) -- (-1.2,-1.4) -- (-1.35,-1.4) ;
\draw [arrows=-] [black,thick,dotted] (-0.25,1.4) -- (-0.4,1.4) -- (-0.4,-1.4) -- (-0.55,-1.4) ;
\draw [arrows=-] [black,thick,dotted] (0.825,1.4) -- (0.675,1.4) -- (.675,-1.4) -- (0.525,-1.4) ;
\draw [arrows=-] [black,thick,dotted] (1.625,1.4) -- (1.475,1.4) -- (1.475,-1.4) -- (1.325,-1.4);
\draw [arrows=-] [black,thick,dotted] (2.425,1.4) -- (2.275,1.4) -- (2.275,-1.4) -- (2.125,-1.4);
\draw [arrows=-] [black,thick,dotted] (3.525,1.4) -- (3.375,1.4) -- (3.375,-1.4) -- (3.225,-1.4);
\node[black,anchor=north] at (-3.75,1.95) { \sffamily x$_{\mathsf{3}}$};
\node[black,anchor=north] at (-2.95,1.95) { \sffamily y$_{\mathsf{3}}$};
\node[black,anchor=north] at (-1.85,1.95) { \sffamily z$_{\mathsf{3}}$};
\node[black,anchor=north] at (-1.05,1.95) { \sffamily x$_{\mathsf{2}}$};
\node[black,anchor=north] at (-0.25,1.95) { \sffamily y$_{\mathsf{2}}$};
\node[black,anchor=north] at (0.825,1.95) { \sffamily z$_{\mathsf{2}}$};
\node[black,anchor=north] at (1.625,1.95) { \sffamily x$_{\mathsf{1}}$};
\node[black,anchor=north] at (2.425,1.95) { \sffamily y$_{\mathsf{1}}$};
\node[black,anchor=north] at (3.525,1.95) { \sffamily z$_{\mathsf{1}}$};
\node[black,anchor=south] at (-4.05,-2) { \sffamily a$_{\mathsf{1}}$};
\node[black,anchor=south] at (-3.25,-2) { \sffamily b$_{\mathsf{1}}$};
\node[black,anchor=south] at (-2.15,-2) { \sffamily c$_{\mathsf{1}}$};
\node[black,anchor=south] at (-1.35,-2) { \sffamily a$_{\mathsf{2}}$};
\node[black,anchor=south] at (-0.55,-2) { \sffamily b$_{\mathsf{2}}$};
\node[black,anchor=south] at (0.525,-2) { \sffamily c$_{\mathsf{2}}$};
\node[black,anchor=south] at (1.325,-2) { \sffamily a$_{\mathsf{3}}$};
\node[black,anchor=south] at (2.155,-2) { \sffamily b$_{\mathsf{3}}$};
\node[black,anchor=south] at (3.225,-2) { \sffamily c$_{\mathsf{3}}$};
\draw [black,thick] (-5.75,1.4) -- (-6,1.4) -- (-6,-1.4) -- (-5.75,-1.4);
\draw [black,thick] (5.75,1.4) -- (6,1.4) -- (6,-1.4) -- (5.75,-1.4);
\node[black,anchor=north] at (6.5,1.75) { \sffamily 2H$^{+}$};
\end{tikzpicture} }
\caption{text}
\label{fig:frag}
\end{figure}
\begin{figure}[!htbp]
\centering
\scalebox{0.65}{
\begin{tikzpicture}[] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (15,6);
\draw [black,-latex new, arrow head=3mm] (0.8,0) -- (8,0);
\node[black] at (7,-0.35) { \sffamily m/z};
\draw [black,-latex new, arrow head=3mm] (1,-0.2) -- (1,4);
\node[black,rotate=90] at (0.5,2.5) { \sffamily Intensity};
%b-series
%b1
%-
%b2
\draw [black] (1.870713,0) -- (1.870713,2.25);
\node[black,anchor=south] at (1.870713,2.25) { \sffamily \Large b$_{\mathsf{2}}$};
%b3
\draw [black] (3.431724,0) -- (3.431724,1.75);
\node[black,anchor=south] at (3.431724,1.75) { \sffamily \Large b$_{\mathsf{3}}$};
%b4
\draw [black] (5.292518,0) -- (5.292518,3);
\node[black,anchor=south] at (5.292518,3) { \sffamily \Large b$_{\mathsf{4}}$};
%b5
\draw [black] (6.423358,0) -- (6.423358,1.5);
\node[black,anchor=south] at (6.423358,1.5) { \sffamily \Large b$_{\mathsf{5}}$};
%b6
%-
%y-series
%y6
%-
%y5
\draw [black] (6.593624,0) -- (6.593624,1);
\node[black,anchor=south] at (7,1) { \sffamily \Large y$_{\mathsf{5}}$};
%y4
\draw [black] (5.883253,0) -- (5.883253,2.25);
\node[black,anchor=south] at (5.883253,2.25) { \sffamily \Large y$_{\mathsf{4}}$};
%y3
\draw [black] (4.322241,0) -- (4.322241,2.5);
\node[black,anchor=south] at (4.322241,2.5) { \sffamily \Large y$_{\mathsf{3}}$};
%y2
\draw [black] (2.461448,0) -- (2.461448,2.75);
\node[black,anchor=south] at (2.461448,2.75) { \sffamily \Large y$_{\mathsf{2}}$};
%y1
\draw [black] (1.330608,0) -- (1.330608,1.5);
\node[black,anchor=south] at (1.330608,1.5) { \sffamily \Large y$_{\mathsf{1}}$};
\node[black,anchor=west] at (11,4.5) { \sffamily \Large b$_{\mathsf{1}}$\phantom{A}D\phantom{AA}ARWIN\phantom{A}y$_{\mathsf{5}}$};
\node[black,anchor=west] at (11,3.5) { \sffamily \Large b$_{\mathsf{2}}$\phantom{A}DA\phantom{AA}RWIN\phantom{A}y$_{\mathsf{4}}$};
\node[black,anchor=west] at (11,2.5) { \sffamily \Large b$_{\mathsf{3}}$\phantom{A}DAR\phantom{AA}WIN\phantom{A}y$_{\mathsf{3}}$};
\node[black,anchor=west] at (11,1.5) { \sffamily \Large b$_{\mathsf{4}}$\phantom{A}DARW\phantom{AA}IN\phantom{A}y$_{\mathsf{2}}$};
\node[black,anchor=west] at (11,0.5) { \sffamily \Large b$_{\mathsf{5}}$\phantom{A}DARWI\phantom{AA}N\phantom{A}y$_{\mathsf{1}}$};
\draw [black,latex new-latex new, arrow head=3mm] (2.461448,4) -- (4.322241,4);
\draw [black,latex new-latex new, arrow head=3mm] (3.431724,4.5) -- (5.292518,4.5);
\end{tikzpicture}}
\caption{text}
\label{fig:denovo}
\end{figure}
\begin{figure}[!htbp]
\centering
\scalebox{0.4}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (20,15);
\draw [black,-latex new, arrow head=3mm] (0.8,5) -- (8,5);
%\node[black] at (7,5.35) { \sffamily m/z};
\draw [black,-latex new, arrow head=3mm] (1,4.8) -- (1,8);
%\node[black,rotate=90] at (0.5,6.5) { \sffamily Intensity};
\draw [black] (1.870713,5) -- (1.870713,7.25);
\draw [black] (3.431724,5) -- (3.431724,6.75);
\draw [black] (5.292518,5) -- (5.292518,8);
\draw [black] (6.423358,5) -- (6.423358,6.5);
\draw [black] (6.593624,5) -- (6.593624,6);
\draw [black] (5.883253,5) -- (5.883253,7.25);
\draw [black] (4.322241,5) -- (4.322241,7.5);
\draw [black] (2.461448,5) -- (2.461448,7.75);
\draw [black] (1.330608,5) -- (1.330608,6.5);
%DARWIN
\draw [black,-latex new, arrow head=3mm] (15.8,10) -- (23,10);
%\node[black] at (22,10.35) { \sffamily m/z};
\draw [black,-latex new, arrow head=3mm] (16,9.8) -- (16,13);
%\node[black,rotate=90] at (15.5,11.4) { \sffamily Intensity};
\draw [black] (16.870713,10) -- (16.870713,12.25);
\draw [black] (18.431724,10) -- (18.431724,11.75);
\draw [black] (20.292518,10) -- (20.292518,13);
\draw [black] (21.423358,10) -- (21.423358,11.5);
\draw [black] (21.593624,10) -- (21.593624,11);
\draw [black] (20.883253,10) -- (20.883253,12.25);
\draw [black] (19.322241,10) -- (19.322241,12.5);
\draw [black] (17.461448,10) -- (17.461448,12.75);
\draw [black] (16.330608,10) -- (16.330608,11.5);
\node[black,anchor=west] at (17.5,13.75) { \sffamily \Huge DARWIN};
\draw [black,dotted,-latex new, arrow head=6mm] (23.5,11) -- (26.5,11);
\node[black,anchor=west] at (27,11.25) { \sffamily \Huge best match};
%ARCHIMEDES
\draw [black,-latex new, arrow head=3mm] (15.8,5) -- (23,5);
%\node[black] at (22,5.35) { \sffamily m/z};
\draw [black,-latex new, arrow head=3mm] (16,4.8) -- (16,8);
%\node[black,rotate=90] at (15.5,6.5) { \sffamily Intensity};
\draw [black] (16.5,5) -- (16.5,7.25);
\draw [black] (18,5) -- (18,6.75);
\draw [black] (20,5) -- (20,7.5);
\draw [black] (21,5) -- (21,6.5);
\draw [black] (21.5,5) -- (21.5,6);
\draw [black] (19.5,5) -- (19.5,7.25);
\draw [black] (19,5) -- (19,7.5);
\draw [black] (17,5) -- (17,7.75);
\draw [black] (16.25,5) -- (16.25,6.5);
\node[black,anchor=west] at (16.5,8.55) { \sffamily \Huge ARCHIMEDES};
%EINSTEIN
\draw [black,-latex new, arrow head=3mm] (15.8,0) -- (23,0);
%\node[black] at (22,0.35) { \sffamily m/z};
\draw [black,-latex new, arrow head=3mm] (16,-0.2) -- (16,3);
%\node[black,rotate=90] at (15.5,1.5) { \sffamily Intensity};
\draw [black] (16.75,0) -- (16.75,2.25);
\draw [black] (18,0) -- (18,1);
\draw [black] (20,0) -- (20,2);
\draw [black] (21,0) -- (21,2);
\draw [black] (21.25,0) -- (21.25,1);
\draw [black] (20.75,0) -- (20.75,1.25);
\draw [black] (18.5,0) -- (18.5,2.5);
\draw [black] (17,0) -- (17,2.75);
\draw [black] (16.5,0) -- (16.5,1.5);
\node[black,anchor=west] at (17.5,3.5) { \sffamily \Huge EINSTEIN};
\draw [black,latex new-latex new, arrow head=6mm] (8.5,6.5) -- (13.5,11);
\draw [black,latex new-latex new, arrow head=6mm] (8.5,6) -- (13.5,6);
\draw [black,latex new-latex new, arrow head=6mm] (8.5,5.5) -- (13.5,1);
\draw [black] (19.25,15) ellipse (5cm and 0.5cm);
\draw [black] (14.25,0) -- (14.25,15);
\draw [black] (24.25,0) -- (24.25,15);
\draw[black] (17.25,0) +(180:3) arc (180:360:5 and 0.5) ;
\end{tikzpicture}}
\caption{text}\label{fig:spectral}
\end{figure}
\begin{figure}[!htbp]
\centering
\scalebox{0.4}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (20,15);
\draw [black,-latex new, arrow head=3mm] (0.8,5) -- (8,5);
%\node[black] at (7,5.35) { \sffamily m/z};
\draw [black,-latex new, arrow head=3mm] (1,4.8) -- (1,8);
%\node[black,rotate=90] at (0.5,6.5) { \sffamily Intensity};
\draw [black] (1.870713,5) -- (1.870713,7.25);
\draw [black] (3.431724,5) -- (3.431724,6.75);
\draw [black] (5.292518,5) -- (5.292518,8);
\draw [black] (6.423358,5) -- (6.423358,6.5);
\draw [black] (6.593624,5) -- (6.593624,6);
\draw [black] (5.883253,5) -- (5.883253,7.25);
\draw [black] (4.322241,5) -- (4.322241,7.5);
\draw [black] (2.461448,5) -- (2.461448,7.75);
\draw [black] (1.330608,5) -- (1.330608,6.5);
%DARWIN
\draw [black,-latex new, arrow head=3mm] (15.8,10) -- (23,10);
%\node[black] at (22,10.35) { \sffamily m/z};
\draw [black,-latex new, arrow head=3mm] (16,9.8) -- (16,13);
%\node[black,rotate=90] at (15.5,11.4) { \sffamily Intensity};
\draw [black] (16.870713,10) -- (16.870713,12.5);
\draw [black] (18.431724,10) -- (18.431724,12.5);
\draw [black] (20.292518,10) -- (20.292518,12.5);
\draw [black] (21.423358,10) -- (21.423358,12.5);
\draw [black] (21.593624,10) -- (21.593624,12.5);
\draw [black] (20.883253,10) -- (20.883253,12.5);
\draw [black] (19.322241,10) -- (19.322241,12.5);
\draw [black] (17.461448,10) -- (17.461448,12.5);
\draw [black] (16.330608,10) -- (16.330608,12.5);
%ARCHIMEDES
\draw [black,-latex new, arrow head=3mm] (15.8,5) -- (23,5);
%\node[black] at (22,5.35) { \sffamily m/z};
\draw [black,-latex new, arrow head=3mm] (16,4.8) -- (16,8);
%\node[black,rotate=90] at (15.5,6.5) { \sffamily Intensity};
\draw [black] (16.5,5) -- (16.5,7.5);
\draw [black] (18,5) -- (18,7.5);
\draw [black] (20,5) -- (20,7.5);
\draw [black] (21,5) -- (21,7.5);
\draw [black] (21.5,5) -- (21.5,7.5);
\draw [black] (19.5,5) -- (19.5,7.5);
\draw [black] (19,5) -- (19,7.5);
\draw [black] (17,5) -- (17,7.5);
\draw [black] (16.25,5) -- (16.25,7.5);
%EINSTEIN
\draw [black,-latex new, arrow head=3mm] (15.8,0) -- (23,0);
%\node[black] at (22,0.35) { \sffamily m/z};
\draw [black,-latex new, arrow head=3mm] (16,-0.2) -- (16,3);
%\node[black,rotate=90] at (15.5,1.5) { \sffamily Intensity};
\draw [black] (16.75,0) -- (16.75,2.5);
\draw [black] (18,0) -- (18,2.5);
\draw [black] (20,0) -- (20,2.5);
\draw [black] (21,0) -- (21,2.5);
\draw [black] (21.25,0) -- (21.25,2.5);
\draw [black] (20.75,0) -- (20.75,2.5);
\draw [black] (18.5,0) -- (18.5,2.5);
\draw [black] (17,0) -- (17,2.5);
\draw [black] (16.5,0) -- (16.5,2.5);
%\draw [black,dotted,arrows=<->] (8.5,6.5) -- (13.5,11);
\draw [black,latex new-latex new, arrow head=6mm] (8.5,6) -- (13.5,6);
\draw [black,latex new-latex new, arrow head=6mm] (8.5,5.5) -- (13.5,1);
\draw [black,latex new-latex new, arrow head=6mm] (8.5,6.5) -- (13.5,11) node [left,near end,text width=4cm,text height=0.8cm] {\sffamily \Huge best match
\\
\phantom{text}};
\draw [black] (32.25,8.5) ellipse (4cm and 0.5cm);
\draw [black] (28.25,3.5) -- (28.25,8.5);
\draw [black] (36.25,3.5) -- (36.25,8.5);
\draw[black] (31.25,3.5) +(180:3) arc (180:360:4 and 0.5) ;
\node[black,anchor=west] at (30,7) { \sffamily \Huge DARWIN};
\node[black,anchor=west] at (30,6) { \sffamily \Huge ARCHIMEDES};
\node[black,anchor=west] at (30,5) { \sffamily \Huge EINSTEIN};
\node[black,anchor=west] at (30,4) { \sffamily \Huge ...};
\draw [black,-latex new, arrow head=6mm] (28,7) -- (24,11);
\draw [black,-latex new, arrow head=6mm] (28,6) -- (24,6);
\draw [black,-latex new, arrow head=6mm] (28,5) -- (24,1);
\end{tikzpicture}}
\caption{text}
\label{fig:proteindatabase}
\end{figure}
\begin{figure}[!htbp]
\centering
\scalebox{0.4}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (20,15);
\draw [black,arrows=->] (0.8,5) -- (8,5);
%\node[black] at (7,5.35) { \sffamily m/z};
\draw [black,arrows=->] (1,4.8) -- (1,8);
%\node[black,rotate=90] at (0.5,6.5) { \sffamily Intensity};
\draw [black] (1.870713,5) -- (1.870713,7.25);
\draw [black] (3.431724,5) -- (3.431724,6.75);
\draw [black] (5.292518,5) -- (5.292518,8);
\draw [black] (6.423358,5) -- (6.423358,6.5);
\draw [black] (6.593624,5) -- (6.593624,6);
\draw [black] (5.883253,5) -- (5.883253,7.25);
\draw [black] (4.322241,5) -- (4.322241,7.5);
\draw [black] (2.461448,5) -- (2.461448,7.75);
\draw [black] (1.330608,5) -- (1.330608,6.5);
\draw [black] (17.25,10.5) ellipse (4cm and 0.5cm);
\draw [black] (13.25,2) -- (13.25,10.5);
\draw [black] (21.25,2) -- (21.25,10.5);
\draw[black] (16.25,2) +(180:3) arc (180:360:4 and 0.5) ;
\draw[black] (16.25,6.1) +(180:3) arc (180:360:4 and 0.5) ;
\node[black,anchor=west] at (15,9) { \sffamily \Huge DARWIN};
\node[black,anchor=west] at (15,8) { \sffamily \Huge ARCHIMEDES};
\node[black,anchor=west] at (15,7) { \sffamily \Huge EINSTEIN};
\node[black,anchor=west] at (15,6) { \sffamily \Huge ...};
\node[black,anchor=west] at (15,5) { \sffamily \Huge NIWRAD};
\node[black,anchor=west] at (15,4) { \sffamily \Huge SEDEMIHCRA};
\node[black,anchor=west] at (15,3) { \sffamily \Huge NIETSNIE};
\node[black,anchor=west] at (15,2) { \sffamily \Huge ...};
\node[black,anchor=west] at (25,10) { \sffamily \Huge PSM};
\node[black,anchor=west] at (25,9) { \sffamily \Huge DARWIN};
\node[black,anchor=west] at (25,8) { \sffamily \Huge ARCHIMEDES};
\node[black,anchor=west] at (25,7) { \sffamily \Huge NIWRAD};
\node[black,anchor=west] at (25,6) { \sffamily \Huge EINSTEIN};
\node[black,anchor=west] at (25,5) { \sffamily \Huge SEDEMIHCRA};
\node[black,anchor=west] at (25,4) { \sffamily \Huge NIETSNIE};
\node[black,anchor=west] at (25,3) { \sffamily \Huge ...};
\node[black,anchor=center] at (32.5,10) { \sffamily \Huge Score};
\node[black,anchor=east] at (33,9) { \sffamily \Huge 10};
\node[black,anchor=east] at (33,8) { \sffamily \Huge 8};
\node[black,anchor=east] at (33,7) { \sffamily \Huge 6};
\node[black,anchor=east] at (33,6) { \sffamily \Huge 4};
\node[black,anchor=east] at (33,5) { \sffamily \Huge 2};
\node[black,anchor=east] at (33,4) { \sffamily \Huge 1};
\node[black,anchor=east] at (33,3) { \sffamily \Huge ...};
\draw [black,-latex new, arrow head=6mm] (21.5,6.1) -- (24,6.1);
\draw [black,-latex new, arrow head=6mm] (8.5,6.1) -- (12,4);
\draw [black,-latex new, arrow head=6mm] (8.5,6.1) -- (12,8) ;
\draw [black] (24.5,9.5) -- (34,9.5);
\draw [black,dashed] (24.5,5.5) -- (34,5.5);
\node[black,anchor=west] at (34.75,5.5) { \sffamily \Huge $T_{s}$};
%\node[black,anchor=west] at (25,1.5) { \sffamily \Huge FDR = ${N_{decoy\ T_{s}}}/{N_{target\ T_{s}}}$};
\end{tikzpicture}}
\scalebox{0.65}{
\begin{tikzpicture}
%\draw [black,-latex new, arrow head=6mm] (7,3) -- (8,4);
\node[black,anchor=west] at (-13,1) { \sffamily \Large };
\node[black,anchor=north west] at (1,1.5) { \sffamily \Large FDR = ${N_{decoy}\ (T_{s})}/{N_{target}\ (T_{s})}$};
\end{tikzpicture}}
\caption{text}
\label{fig:targetdecoy}
\end{figure}%
\begin{figure}[!htbp]
\centering
\scalebox{0.4}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (20,15);
\draw [black,arrows=->] (0.8,5) -- (8,5);
%\node[black] at (7,5.35) { \sffamily m/z};
\draw [black,arrows=->] (1,4.8) -- (1,8);
%\node[black,rotate=90] at (0.5,6.5) { \sffamily Intensity};
\draw [black] (1.870713,5) -- (1.870713,7.25);
\draw [black] (3.431724,5) -- (3.431724,6.75);
\draw [black] (5.292518,5) -- (5.292518,8);
\draw [black] (6.423358,5) -- (6.423358,6.5);
\draw [black] (6.593624,5) -- (6.593624,6);
\draw [black] (5.883253,5) -- (5.883253,7.25);
\draw [black] (4.322241,5) -- (4.322241,7.5);
\draw [black] (2.461448,5) -- (2.461448,7.75);
\draw [black] (1.330608,5) -- (1.330608,6.5);
\draw [black] (17.25,10.5) ellipse (4cm and 0.5cm);
\draw [black,dotted] (13.25,2) -- (13.25,6.1);
\draw [black] (13.25,6.1) -- (13.25,10.5);
\draw [black,dotted] (21.25,2) -- (21.25,6.1);
\draw [black] (21.25,6.1) -- (21.25,10.5);
\draw[black,dotted] (16.25,2) +(180:3) arc (180:360:4 and 0.5) ;
\draw[black] (16.25,6.1) +(180:3) arc (180:360:4 and 0.5) ;
\node[black,anchor=west] at (15,9) { \sffamily \Huge DARWIN};
\node[black,anchor=west] at (15,8) { \sffamily \Huge ARCHIMEDES};
\node[black,anchor=west] at (15,7) { \sffamily \Huge EINSTEIN};
\node[black,anchor=west] at (15,6) { \sffamily \Huge ...};
\node[black,anchor=west] at (15,5) { \sffamily \Huge NIWRAD};
\node[black,anchor=west] at (15,4) { \sffamily \Huge SEDEMIHCRA};
\node[black,anchor=west] at (15,3) { \sffamily \Huge NEITSNIE};
\node[black,anchor=west] at (15,2) { \sffamily \Huge ...};
\draw [dotted,black,-latex new, arrow head=6mm] (8.5,6.1) -- (12,4);
\draw [black,-latex new, arrow head=6mm] (8.5,6.1) -- (12,8) ;
\draw [black,-latex new, arrow head=6mm] (21.5,6.1) -- (24,6.1);
\node[black,anchor=west] at (13,1) { \sffamily \large };
\end{tikzpicture}}
%\hspace{0.3cm}
\scalebox{0.65}{
\begin{tikzpicture}[
declare function={gamma(\z)=
2.506628274631*sqrt(1/\z)+ 0.20888568*(1/\z)^(1.5)+ 0.00870357*(1/\z)^(2.5)- (174.2106599*(1/\z)^(3.5))/25920- (715.6423511*(1/\z)^(4.5))/1244160)*exp((-ln(1/\z)-1)*\z;},
declare function={gammapdf(\x,\k,\theta) = 1/(\theta^\k)*1/(gamma(\k))*\x^(\k-1)*exp(-\x/\theta);}
]
\newcommand\gauss[2]{1/(#2*sqrt(2*pi))*exp(-((x-#1)^2)/(2*#2^2))}
%\draw[help lines] (0,0) grid (20,5);
%X-axis
\draw [very thick, black,-latex new, arrow head=3mm] (-0.2,0.46) -- (7,0.46);
\node[black,anchor=west] at (6,0) { \sffamily \large S};
%Y-axis
\draw [very thick, black,-latex new, arrow head=3mm] (0,0.26) -- (0,6);
\node[black,anchor=west,rotate=90] at (-0.375,3) { \sffamily \large \# spectra};
\node[black,anchor=west] at (2,5) { \sffamily \Large incorrect PSMs};
\draw [very thick, black,dotted] (1.2,4) -- (2,4.75);
\node[black,anchor=west] at (2,3) { \sffamily \Large correct PSMs};
\draw [very thick, black,dotted] (4.5,1) -- (5,2.8);
\draw [very thick, black] (0.4,0.46) -- (0.54,3) -- (0.65,2.8) -- (0.9,5.5) -- (1,5.6) -- (1.4,4) -- (1.5,3) -- (1.6,2) -- (1.8,1) -- (2.2,1.4) -- (2.4,1.3) -- (2.6,1.5) -- (2.7,1.4) -- (3,1.8) -- (3.3,2) -- (3.6,1.7) -- (3.8,1.8) -- (4,1.6) -- (4.2,1.7) -- (4.5,1.3) -- (5,1) -- (6,0.46);
%\draw [black] (2,0.4) to [out=30,in=150] (6,0.4);
\begin{axis}[axis lines=none,samples=50]
\addplot [thick,dashed,smooth, domain=0:40, black] {gammapdf(x,5,0.75)};
\addplot[thick,dashed,smooth, domain=0:40, black] {\gauss{20}{6}};
\end{axis}
\end{tikzpicture}}
\scalebox{0.65}{
\begin{tikzpicture}
%\draw [black,-latex new, arrow head=6mm] (7,3) -- (8,4);
\node[black,anchor=west] at (-5,4) { \sffamily \Large };
\node[black,anchor=north west] at (1,3.5) { \sffamily \Large FDR = $N_{inc}(P_{T})/N(P_{T})$};
\node[black,anchor=north west] at (8.5,3.5) { \sffamily \Large $N_{inc}(P_{T})$ = $\sum\limits_{{x|P_{x}\geq P_{T}}}(1 - P_{x}$)};
\node[black,anchor=north west] at (8.5,2) { \sffamily \Large $N(P_{T})$ = $\sum\limits_{{x|P_{x}\geq P_{T}}}1$};
\end{tikzpicture}}
\caption{text}
\label{fig:peptideprophet}
\end{figure}
\begin{figure}[!htbp]
\centering
\scalebox{0.9}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
%\draw[help lines] (0,0) grid (15,15);
\node[black] at (0,4) { \sffamily Protein A};
\node[black] at (0,3.5) { \sffamily Protein B};
\node[black] at (2,4.5) { \sffamily Peptide 1};
\node[black] at (4,4.5) { \sffamily Peptide 2};
\node[black] at (6,4.5) { \sffamily Peptide 3};
\draw [black,fill=black] (3,4) circle [radius=0.1];
\draw [black,fill=black] (5,4) circle [radius=0.1];
\draw [black,fill=black] (7,4) circle [radius=0.1];
\draw [black,fill=black] (5,3.5) circle [radius=0.1];
\draw [black,fill=black] (7,3.5) circle [radius=0.1];
\node[black] at (10.5,6) { \sffamily 1 a. Prob Protein A = 1};
\node[black] at (11,5.5) { \sffamily Peptide 1 $\rightarrow$ w = 1};
\node[black] at (11,5) { \sffamily Peptide 2 $\rightarrow$ w = 1 };
\node[black] at (11,4.5) { \sffamily Peptide 3 $\rightarrow$ w = 1 };
\node[black] at (10.5,3.5) { \sffamily 1 b. Prob Protein B = 0};
\node[black] at (11,3) { \sffamily Peptide 2 $\rightarrow$ w = 0 };
\node[black] at (11,2.5) { \sffamily Peptide 3 $\rightarrow$ w = 0 };
\end{tikzpicture}}
\caption{text}
\label{fig:weight}
\end{figure}
%%%%%%%%%%%%%%%%%% Objectives %%%%%%%%%%%%%%%%
\newpage{\thispagestyle{empty}\cleardoublepage}
\chapter{Rationale and Objectives} \label{chap:objectives}
\lettergroup{\thechapter}
text
%%%%%%%%%%%%%%%%%% FDR %%%%%%%%%%%%%%%%
\newpage{\thispagestyle{empty}\cleardoublepage}
\chapter{Partially Sequenced Organisms, Decoy Searches and False Discovery Rates}
\label{chap:FDR}\lettergroup{\thechapter}
\begin{quote}
\textbf{Abstract:} text
\end{quote}
\vfill
Adapted from:\\
\textbf{Victor, B.}, Gabri\"el, S., Kanobana, K., Mostovenko, E., Polman, K., Dorny, P., Deelder, A. M., and Palmblad, M. Partially Sequenced Organisms, Decoy Searches and False Discovery Rates. \textit{Journal of Proteome Research} 11, 3 (2012), 1991--1995.
\newpage
text
\newpage{\thispagestyle{empty}\cleardoublepage}
\chapter{Proteomic Analysis of \textit{Taenia solium} Metacestode Excretion/Secretion Proteins}
\label{chap:ESP} \lettergroup{\thechapter}
\begin{quote}
\textbf{Abstract:} text
\end{quote}
\vfill
Adapted from:\\
\textbf{Victor, B.}, Kanobana, K., Gabri\"el, S., Polman, K., Deckers, N., Dorny, P., Deelder, A. M., and Palmblad, M. Proteomic Analysis of \textit{Taenia solium} Metacestode Excretion/Secretion Proteins. \textit{Proteomics} 12, 11 (2012), 1860--1869.
\newpage
text
\newpage{\thispagestyle{empty}\cleardoublepage}
\chapter{Use of Expressed Sequence Tags for the Identification of \textit{Taenia solium} Metacestode Excretion/Secretion Proteins}
\chaptermark{Use of ESTs for the Identification of \textit{T. solium} Metacestode ESPs.}
\label{chap:EST} \lettergroup{\thechapter}
\begin{quote}
\textbf{Abstract:} text
\end{quote}
\vfill
Adapted from:\\
\textbf{Victor, B.}, Dorny, P., Kanobana, K., Polman, K., Lindh, J., Deelder, A. M., Palmblad, M., and Gabri\"el, S. Use of Expressed Sequence Tags as an Alternative Approach for the Identification of \textit{Taenia solium} Metacestode Excretion/Secretion Proteins. \textit{BMC Research Notes} 6, 1 (2013), 224.
\newpage
text
\newpage{\thispagestyle{empty}\cleardoublepage}
\chapter{The Search for Differential Proteins}
\label{chap:diffproteins}\lettergroup{\thechapter}
\begin{figure}[!htbp]
\centering
{\sffamily
\begin{tikzpicture}
\tikzstyle{every node}=[anchor=center]
\tikzstyle{column 3}=[text width=0.3\linewidth,text centered]
\tikzstyle{column 2}=[text width=0.3\linewidth,text centered]
\tikzstyle{column 1}=[text width=0.3\linewidth,text centered]
\matrix [row sep=0.2cm,column sep=0.5cm] %draw
{
\node()[]{}; & \node(vc)[]{tandem mass spectro-\\metry analysis of \textit{Taenia} excretion/secretion proteins}; &\node()[]{}; \\
\node(v1)[]{all \textit{Taenia}\\ \textit{solium} spectra}; & &\node(v3)[]{all \textit{Taenia}\\ \textit{hydatigena} spectra}; \\
& \node(v5)[]{host proteins and \\common contaminations}; &\\
\node(v7){spectral\\ quality filter};& & \node(v9)[]{spectral\\ quality filter}; \\
& \node(v11)[]{non-peptide and \\low quality spectra}; &\\
\node(v13){high quality \textit{Taenia}\\ \textit{solium} spectra}; & \node(v14){}; & \node(v15){high quality \textit{Taenia}\\ \textit{hydatigena} spectra}; \\
\node(){}; & \node(va){spectra are binned prior to spectral comparison}; & \node(){}; \\
\node(v16){spectrum 1: \centering
\scalebox{0.25}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
\draw [black,-latex new, arrow head=3mm] (0.8,5) -- (8,5);
\draw [black,-latex new, arrow head=3mm] (1,4.8) -- (1,8);
\draw [black] (1.5,5) rectangle (2,6);
\draw [black] (2,5) rectangle (2.5,6.5);
\draw [black] (2.5,5) rectangle (3,6.5);
\draw [black] (3,5) rectangle (3.5,8);
\draw [black] (3.5,5) rectangle (4,7);
\draw [black] (4,5) rectangle (4.5,6.5);
\draw [black] (4.5,5) rectangle (5,7.5);
\draw [black] (5,5) rectangle (5.5,7);
\draw [black] (5.5,5) rectangle (6,5.5);
\draw [black] (6,5) rectangle (6.5,6);
\draw [black] (6.5,5) rectangle (7,5.5);
\end{tikzpicture}}}; & \node(v17){}; & \node(v18){spectrum 1: \centering
\scalebox{0.25}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
\draw [black,-latex new, arrow head=3mm] (0.8,5) -- (8,5);
\draw [black,-latex new, arrow head=3mm] (1,4.8) -- (1,8);
\draw [black] (1.5,5) rectangle (2,6);
\draw [black] (2,5) rectangle (2.5,6.5);
\draw [black] (2.5,5) rectangle (3,6.5);
\draw [black] (3,5) rectangle (3.5,8);
\draw [black] (3.5,5) rectangle (4,7);
\draw [black] (4,5) rectangle (4.5,6.5);
\draw [black] (4.5,5) rectangle (5,7.5);
\draw [black] (5,5) rectangle (5.5,7);
\draw [black] (5.5,5) rectangle (6,5.5);
\draw [black] (6,5) rectangle (6.5,6);
\draw [black] (6.5,5) rectangle (7,5.5);
\end{tikzpicture}}}; \\
\node(v19){spectrum 2: \centering
\scalebox{0.25}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
\draw [black,-latex new, arrow head=3mm] (0.8,5) -- (8,5);
\draw [black,-latex new, arrow head=3mm] (1,4.8) -- (1,8);
\draw [black] (1.5,5) rectangle (2,6);
\draw [black] (2,5) rectangle (2.5,7.5);
\draw [black] (2.5,5) rectangle (3,7);
\draw [black] (3,5) rectangle (3.5,7.25);
\draw [black] (3.5,5) rectangle (4,7);
\draw [black] (4,5) rectangle (4.5,6);
\draw [black] (4.5,5) rectangle (5,7.5);
\draw [black] (5,5) rectangle (5.5,5.5);
\draw [black] (5.5,5) rectangle (6,5.75);
\draw [black] (6,5) rectangle (6.5,6);
\draw [black] (6.5,5) rectangle (7,5.5);
\end{tikzpicture}}}; & \node(v20){}; & \node(v21){spectrum 2: \centering
\scalebox{0.25}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
\draw [black,-latex new, arrow head=3mm] (0.8,5) -- (8,5);
\draw [black,-latex new, arrow head=3mm] (1,4.8) -- (1,8);
\draw [black] (1.5,5) rectangle (2,6);
\draw [black] (2,5) rectangle (2.5,6.5);
\draw [black] (2.5,5) rectangle (3,7.5);
\draw [black] (3,5) rectangle (3.5,8);
\draw [black] (3.5,5) rectangle (4,7);
\draw [black] (4,5) rectangle (4.5,6.5);
\draw [black] (4.5,5) rectangle (5,5.5);
\draw [black] (5,5) rectangle (5.5,6);
\draw [black] (5.5,5) rectangle (6,8);
\draw [black] (6,5) rectangle (6.5,6);
\draw [black] (6.5,5) rectangle (7,5.5);
\end{tikzpicture}}}; \\
\node(v25){spectrum 3: ...\phantom{\centering
\scalebox{0.25}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
\draw [black,-latex new, arrow head=3mm] (0.8,5) -- (6.5,5);
\draw [black,-latex new, arrow head=3mm] (1,4.8) -- (1,8);
\end{tikzpicture}}}}; & \node(v26){}; & \node(v27){spectrum 3: ...\phantom{\centering
\scalebox{0.25}{
\begin{tikzpicture}[very thick] %use thick for all figures!!!
\tikzstyle{every node}=[anchor=west]
\draw [black,-latex new, arrow head=3mm] (0.8,5) -- (6.5,5);
\draw [black,-latex new, arrow head=3mm] (1,4.8) -- (1,8);
\end{tikzpicture}}}}; \\
\node(){}; & \node(){\phantom{text}\\ \phantom{text}}; & \node(){}; \\
\node(v28){unique \textit{Taenia}\\ \textit{solium} spectra}; & \node(vb){six reading frame translation of the \\\textit{Taenia solium} genome}; & \node(v30){unique \textit{Taenia}\\ \textit{hydatigena} spectra}; \\
\node(){}; & \node(){all identified peptides +\\ their matching spectra}; & \node(){}; \\
\node(v31){unique \textit{Taenia solium} peptides (proteins)}; & \node(v32){}; & \node(v33){}; \\
};
\draw [-latex new, arrow head=2mm] [black,thick] (vc.west) to [out=180,in=45] (v1.north);
\draw [-latex new, arrow head=2mm] [black,thick] (vc.east) to [out=0,in=135] (v3.north);
\draw [-latex new, arrow head=2mm] [black,thick] (v1.south) -- (v7.north);
\draw [-latex new, arrow head=2mm] [black,thick] (v7.south) -- (v13.north);
\draw [-latex new, arrow head=2mm] [black,thick] (v13.south) -- (v16.north);
\draw [-latex new, arrow head=2mm] [black,thick] (v25.south) -- (v28.north);
\draw [-latex new, arrow head=2mm] [black,thick] (v28.south) -- (v31.north);
\draw [-latex new, arrow head=2mm] [black,thick] (v3.south) -- (v9.north);
\draw [-latex new, arrow head=2mm] [black,thick] (v9.south) -- (v15.north);
\draw [-latex new, arrow head=2mm] [black,thick] (v15.south) -- (v18.north);
\draw [-latex new, arrow head=2mm] [black,thick] (v27.south) -- (v30.north);
\draw [-latex new, arrow head=2mm] [black,thick] (v1.south) to [out=-45,in=180] (v5.west);
\draw [-latex new, arrow head=2mm] [black,thick] (v7.south) to [out=-45,in=180] (v11.west);
\draw [-latex new, arrow head=2mm] [dotted,black,thick] (v1.south) to [out=-45,in=125] (vb.155);
\draw [-latex new, arrow head=2mm] [dotted,black,thick] (vb.-155) to [out=-125,in=90] (v31.north);
\draw [-latex new, arrow head=2mm] [black,thick] (va.west) to [out=180,in=45] (v16.20);
\draw [-latex new, arrow head=2mm] [black,thick] (va.east) to [out=0,in=135] (v18.160);
%\draw [-latex new, arrow head=2mm] [black,thick] (vb.west) to [out=180,in=45] (v31.north);
\draw [-latex new, arrow head=2mm] [black,thick] (v3.south) to [out=-135,in=0] (v5.east);
\draw [-latex new, arrow head=2mm] [black,thick] (v9.south) to [out=-135,in=0] (v11.east);
\draw [latex-latex new, arrow head=2mm,dashed] [black,thick] (v16.east) -- (v18.west);
\draw [latex-latex new, arrow head=2mm,dashed] [black,thick] (v16.east) -- (v21.west);
%\draw [latex-latex new, arrow head=2mm,dashed] [black,thick] (v16.east) -- (v24.west);
\draw [latex-latex new, arrow head=2mm,dashed] [black,thick] (v16.east) -- (v27.west) node[left,midway,text width=1.8cm,text height=1.2cm]{\textcolor{black}{spectral \\comparisons}};
%\draw [-latex new, arrow head=2mm] [black,thick] (v4.south) -- (v11.east) node [right,black,midway,text width=2.8cm,text height=1.2cm] {\textcolor{black}{Proglottids/eggs \\shed with stools}};
%
%\draw [-latex new, arrow head=2mm] [black,thick] (v8.west) -- (v6.south);
%\draw [-latex new, arrow head=2mm] [black,thick] (v11.west) -- (v12.east);
%\draw [-latex new, arrow head=2mm] [black,thick] (v6.north) -- (v2.west);
\end{tikzpicture}}
\caption{text}
\label{fig:spectralcomp}
\end{figure}
\newpage{\thispagestyle{empty}\cleardoublepage}
\chapter{General Discussion}\label{chap:gendiscussion}
\lettergroup{\thechapter}
text
\newpage{\thispagestyle{empty}\cleardoublepage}
\chapter{Bibliography}
\lettergroup{\thechapter}
\begingroup
\def\chapter#1{} % needed because the thumb marks were not triggered for the first page of the biblio...
\small
\singlespace
\bibliographystyle{elsarticle-harv_M2}%elsarticle-harv_M2
\bibliography{ref}
\endgroup
\onehalfspace
\newpage{\thispagestyle{empty}\cleardoublepage}
\chapter{Summary}
\lettergroup{\thechapter}
\newpage{\thispagestyle{empty}\cleardoublepage}
\chapter{Samenvatting}
\lettergroup{\thechapter}
\newpage{\thispagestyle{empty}\cleardoublepage}
\appendix
\chapter{Appendix}
\lettergroup{\thechapter}
\end{document}