Reducing metal-ion mediated adsorption of acidic peptides in RPLC-based assays using hybrid silica chromatographic surfaces.

In this study we evaluate column hardware exhibiting a novel hybrid silica surface in its ability to mitigate metal-induced adsorption artifacts such as chromatographic peak tailing for acidic amino acid residue containing peptides. Using a conventional reversed-phase liquid chromatography (RPLC)-based method, chromatographic performance of a peptide map was compared using a traditional stainless-steel column and an equivalent column bearing a novel hybrid silica surface. Tailing factors for six peptides containing acidic amino acid residues (Tf ≥ 1.50) were observed to be reduced up to 80% to a nominal value Tf ≤ 1.2 with R.S.D. % ≤ 4%. Furthermore, recovery for two of the identified peptides exhibited increased recovery in addition to reduced peak tailing when using the column bearing the hybrid silica surface. Performance was unaffected for peaks where there were no implications of metal induced effects. Collectively, this study demonstrates that the novel hybrid silica surface can effectively reduce peak tailing for acidic residue containing peptides.

Proteogenomic Analysis of Surgically Resected Lung Adenocarcinoma.

INTRODUCTION: Despite apparently complete surgical resection, approximately half of resected early-stage lung cancer patients relapse and die of their disease. Adjuvant chemotherapy reduces this risk by only 5% to 8%. Thus, there is a need for better identifying who benefits from adjuvant therapy, the drivers of relapse, and novel targets in this setting. METHODS: RNA sequencing and liquid chromatography/liquid chromatography-mass spectrometry proteomics data were generated from 51 surgically resected non-small cell lung tumors with known recurrence status. RESULTS: We present a rationale and framework for the incorporation of high-content RNA and protein measurements into integrative biomarkers and show the potential of this approach for predicting risk of recurrence in a group of lung adenocarcinomas. In addition, we characterize the relationship between mRNA and protein measurements in lung adenocarcinoma and show that it is outcome specific. CONCLUSIONS: Our results suggest that mRNA and protein data possess independent biological and clinical importance, which can be leveraged to create higher-powered expression biomarkers.