Proteomics

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Peptide Retention Time Prediction for Electrostatic Repulsion-Hydrophilic Interaction Chromatography


ABSTRACT: Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) is a legacy separation tools developed by Dr. Andrew Alpert and has been used for developing unique separation methods of hydrophilic compounds, including peptides. We employed a proteomics-derived ~170,000 peptide retention dataset to evaluate major ERLIC retention features using the framework of our Sequence-Specific Retention Calculator model. Separation conditions were adjusted to obtain a wider proteome coverage, particularly for non-modified peptides, resulting in a superior separation orthogonality for a 2D LC combination with reversed-phase C18 LC-MS in the second dimension. The SSRCalc ERLIC model coefficients elucidated known ERLIC retention mechanisms, reflecting a dependence on peptide orientation and the position of charged and hydrophilic residues across the peptide backbone. R2 values of 0.935 and 0.955 accuracy were demonstrated for the standard interpretable SSRCalc model and a GRU-based machine learning algorithm, respectively. The effects of various PTMs on peptide retention were evaluated in this study, covering spontaneous (oxidation, deamidation) and enzymatic (N-terminal acetylation, phosphorylation, glycosylation) modifications.

INSTRUMENT(S): timsTOF Pro 2

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Oleg Krokhin  

PROVIDER: MSV000095965 | MassIVE |

REPOSITORIES: MassIVE

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