1 Introduction

Our pipeline, MICSQTL, integrates RNA and protein expressions to detect potential cell marker proteins and estimate cell abundance in mixed proteomes without a reference signature matrix. MICSQTL enables cell-type-specific quantitative trait loci (QTL) mapping for proteins or transcripts using bulk expression data and estimated cellular composition per molecule type, eliminating the necessity for single-cell sequencing. We use matched transcriptome-proteome from human brain frontal cortex tissue samples to demonstrate the input and output of our tool.