## 3 Results and Discussion
### Validation of Phosphoprotein Enrichment by the PAPE Procedure
Examples include RD29A (desiccation-responsive protein 29; also known as low-temperature-responsive protein 78, At5g52310), NR2 (nitrate reductase 2, At1g37130) and two proteins with tetratricopeptide repeat (TPR) domains (At1g01320 and At4g28080) (Figure 4). Taken together, these phosphopeptide detection data demonstrate the efficacy of the PAPE procedure to identify (novel) phosphoproteins. Figure 4: Examples of the increased detection of phosphopeptides associated with a particular protein in the PAPE fraction. A progressively increasing number of phosphopeptide detections is seen for the listed proteins from the crude to the PAPE fraction. (Abbreviations: NR2, nitrate reductase 2; RD29, desiccation-responsive protein 29, which is also known as low-temperature-responsive protein 78; TPR-like, proteins from the tetratricopeptide repeat superfamily). \begin{table}
\begin{tabular}{c c c c c c c c c c c} \hline \hline
**No. ** & **Protein code** & **Description** & **Sequence** & **MIP+[Da]** & **q-Value** & **PEP** & **pRS Score** & **\# PSMs** & **pRS Site Probabilities** \\ \hline  & & & em24g251-p24 family/GOLD & SSIVLLLSILSILSPVT & 2,184.20708 & 0.016281 & 0.3789499 & 58 & 11 & 84.3; [S12] 84.6; [T15] \(\times\)0.5; \begin{table}
\begin{tabular}{r c c c c c c c c c c} \hline \hline \multicolumn{1}{c}{**No.**} & **Protein code** & **Description** & **Sequence** & **MH+[Da]** & **q-Value** & **PEP** & **pRS Score** & \# **PSMs** & **pRS Site Probabilities** \\ \hline
1 & AT5G56740.1 & histone acetyltransferase transferase of the GNAT family 2 & LSQILVLPSPGK & 1,509.80133 & 0.011279 & 0.2471017 & 30 & 4 & S(Z): 0.4, S(S): 99.6 \\  & & oxidoreductaseusze, zinc-binding dehydrogenase family protein & NAALATTATTPVL & 1,736.90842 & 0.015443 & 0.4098554 & 40 & 1 & T(6): 12.5; T(7): 12.5; \\  & & CBS domain-containing protein with a domain of & LLDLLIGKRISTLL & 1,885.07854 & 0.023892 & 0.3993647 & 51 & 11 & S(1): 1.7; T(12): 98.3 \\  & & unknown function (DUF21) & PR-loop containing nucleoside & & & & & & \\
4 & AT4G28000.1 & triphosphate hydrolase & HTRNLAPGSK & 1,160.55168 & 0.03559 & 0.754117 & 50 & 3 & T(2): 0.0; S(S): 100.0 \\  & & superfamily protein & & & & & & & \\
5 & AT1G72150.1 & PATELLIN 1 & SSFFVSDFRNAPGL & 2,064.01040 & 0.039425 & 0.6264254 & 39 & 1 & 98.0 \\  & & throwd-tRNA synthetase, putativethreonine-tRNA & SRFGGELGTPVDDL & & & & & & & \\
6 & AT2G04842.1 & putativethreonine-tRNA & NRNIKNAYETR** & 3,067.42545 & 0.041246 & 0.6307821 & 38 & 1 &
\begin{tabular}{} \end{tabular} \\  & & ligase, putative & & & & & & & & \\
7 & AT5G22760.1 & tensm-TS01-like CXC & VIRNSDIFUGDAS & & & & & & \\  & domain-containing protein & K\## & & & & & & & \\  & & & & & & & & & \\  & & & & & & & & & \\  & & & & & & & & & \\  & & & & & & & & & \\  & & & & & & & & & \\
8 & AT4G16155.1 & dihydrodiopyl & DIIATGSVPFVPK & 1,536.80143 & 0.043742 & 0.515806 & 38 & 2 & T(6): 12.3; S(8): 87.7 \\  & & & dehydrodiness & & & & & & \\ \hline \end{tabular}
\end{table} 
Table 1: _Cont._
\begin{table}
\begin{tabular}{c c c c c c c c c c c c} \hline \hline  & **No. ** & **Protein code** & **Description** & **Sequence** & **MIH-[Da]** & **q-Value** & **PEP** & **pRS Score** & **\# PSMs** & **pRS Site Probabilities** \\ \hline  & & & & & & & & & & & & T(3): 13.7; S(5): 57.9; \\  & 1 & ATIG56220.4 & dormancy/auxin associated & HHITSFRPSSGNDOSE & 2