Poster Presentations
Day 1, June 10（Wed.） Room P (5F 501+502)
- 1P-17
Physicochemical Basis of Peptide Detectability Under Different Pretreatment Conditions in LC/MS
(Sysmex)
oHinata Miyanishi, Kota Tanaka, Tetsuro Morinaga, Takashi Kagawa
Optimizing sample pretreatment is a key factor determining the range of proteins and peptides detectable by liquid chromatography–mass spectrometry (LC/MS)–based proteomics. In particular, hydrophobic proteins often exhibit insufficient solubilization and limited enzymatic accessibility, reducing digestion efficiency. Although maltoside-based detergents have been reported to enhance enzymatic digestion efficiency and suppress adsorption to vials, the physicochemical properties of peptides that benefit from such pretreatment remain insufficiently characterized. This study aimed to evaluate pretreatment-dependent peptide recovery from the perspective of peptide physicochemistry and to establish a basis for selecting optimal pretreatment methods through in silico assessment prior to experimentation. Peptides identified under multiple pretreatment conditions were complied, and physicochemical descriptors were calculated using Biopython. Discriminative features associated with peptides uniquely detected under each pretreatment condition were explored, and distributional tendencies were visualized using principal component analysis (PCA). The results revealed characteristic physicochemical tendencies in peptides preferentially detected under specific pretreatment protocols, highlighting the utility of in silico preevaluation in proteomic workflow design.