Antigen interference from residual antigen peptides remains a persistent challenge in anti-peptide immunocapture liquid chromatography-tandem mass spectrometry (IC-LC-MS/MS) assays for quantifying low-abundance protein biomarkers. In this manuscript, we introduce a novel approach that utilizes carrier protein-conjugated, stable isotopically labeled surrogate peptides as antigens to generate anti-peptide polyclonal antibodies (pAbs). By leveraging mass spectrometry to distinguish residual labeled antigen peptides from endogenous peptides, this method effectively eliminates antigen interference in anti-peptide IC-LC-MS/MS assays. This innovative approach significantly advances anti-peptide IC-LC-MS/MS quantitative bioanalysis for targeted proteomics, enabling the detection of low-abundance protein biomarkers at picomolar and sub-picomolar levels.