Multiaspect Examinations of Possible Alternative Mappings of Identified Variant Peptides: A Case Study on the HEK293 Cell Line.

ABSTRACT: Adopting proteogenomics approach to validate single nucleotide variation events by identifying corresponding single amino acid variant peptides from mass spectrometry (MS)-based proteomics data facilitates translational and clinical research. Although variant peptides are usually identified from MS data with a stringent false discovery rate (FDR), FDR control could fail to eliminate dubious results caused by several issues; thus, postexamination to eliminate dubious results is required. However, comprehensive postexaminations of identification results are still lacking. Therefore, we propose a framework of three bottom-up levels, peptide-spectrum match, peptide, and variant event levels, that consists of rigorous 11-aspect examinations from the MS perspective to further confirm the reliabi

SUBMITTER: Choong WK 

PROVIDER: S-EPMC9118379 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature