Final answer:
Selective fractionation methods like PAPE and MOAC are used to enrich and detect phosphoproteins more efficiently, resulting in an increased number of identified phosphopeptides and known phosphoproteins, which serves to better understand the role of protein phosphorylation in biological systems.
Step-by-step explanation:
The increase in specific phosphorus fractions observed in phosphoproteomics studies can be attributed to the selective enrichment processes used in the experiments. For example, phosphopeptides were more abundantly detected in the 40% ammonium sulfate (AS), Metal Oxide Affinity Chromatography (MOAC), and Phosphoprotein Enrichment by Phosphatase Alkaline Precipitation (PAPE) fractions compared to the crude extract, due to these procedures more efficiently precipitating and enriching phosphoproteins. MOAC exhibited unspecific binding, which was alleviated by the PAPE procedure that already enriched for phosphoproteins. The high technical reproducibility of PAPE demonstrated its robustness, showing a higher number of known phosphoproteins compared to the MOAC method, as validated by databases like P3DB, and was further evidenced by Gene Ontology annotations of proteins involved in response to stimuli and stress.
Such selective enrichment techniques are crucial to identify novel phosphopeptides and phosphorylated proteins that might otherwise remain undetected amidst a complex protein mixture. The fractionation steps designed to target phosphoproteins allowed the identification of both known and novel phosphoproteins, reflecting the effectiveness of the PAPE process and providing insights into protein phosphorylation's role in biological processes.