This study presents a comprehensive analysis of the proteome and transcriptome of HeLa cells, a human cervical carcinoma cell line. Using advanced mass spectrometry (MS) and RNA-Seq technologies, the researchers identified 10,255 different human proteins encoded by 9,207 genes, providing a lower limit on the proteome in this cell line. Deep transcriptome sequencing revealed transcripts for nearly all detected proteins. The abundance of >90% of the proteins was found to be within a factor of 60 of the median protein expression level. Comparisons between the proteome and transcriptome, along with analysis of protein complex databases and Gene Ontology (GO) categories, suggest that the study achieved deep coverage of the functional transcriptome and proteome of a single cell type. The results highlight the completeness of the detected proteome, with most macromolecular complexes and metabolic pathways being well-represented. The study also demonstrates the high correlation between transcriptome and proteome data, with many regulatory proteins showing lower expression levels compared to structural proteins. Overall, the findings provide a detailed understanding of the proteomic and transcriptomic landscape of HeLa cells, contributing to the field of systems biology.This study presents a comprehensive analysis of the proteome and transcriptome of HeLa cells, a human cervical carcinoma cell line. Using advanced mass spectrometry (MS) and RNA-Seq technologies, the researchers identified 10,255 different human proteins encoded by 9,207 genes, providing a lower limit on the proteome in this cell line. Deep transcriptome sequencing revealed transcripts for nearly all detected proteins. The abundance of >90% of the proteins was found to be within a factor of 60 of the median protein expression level. Comparisons between the proteome and transcriptome, along with analysis of protein complex databases and Gene Ontology (GO) categories, suggest that the study achieved deep coverage of the functional transcriptome and proteome of a single cell type. The results highlight the completeness of the detected proteome, with most macromolecular complexes and metabolic pathways being well-represented. The study also demonstrates the high correlation between transcriptome and proteome data, with many regulatory proteins showing lower expression levels compared to structural proteins. Overall, the findings provide a detailed understanding of the proteomic and transcriptomic landscape of HeLa cells, contributing to the field of systems biology.