A deep proteome and transcriptome mapping of a human cancer cell line, HeLa, was conducted using advanced mass spectrometry (MS) and RNA-Seq. The study identified 10,255 human proteins from 9,207 genes, with over 90% of the proteins having abundances within a factor of 60 of the median. RNA-Seq data revealed transcripts for nearly all detected proteins, with 11,936 protein-coding genes detected, including many low-abundance transcripts. The proteome and transcriptome data showed a high degree of correlation, with the proteome covering a large portion of the functional transcriptome. The study also demonstrated that the proteome was highly complete, with over 90% of the proteins within a factor of 60 of the median abundance. The data suggest that at least 10,000–12,000 genes are expressed in HeLa cells. The study provides a comprehensive view of the proteome and transcriptome of a human cancer cell line, highlighting the importance of systems biology approaches in understanding cellular functions. The results demonstrate the potential of high-resolution MS and RNA-Seq in achieving a deep understanding of the proteome and transcriptome of a single cell type. The study also highlights the importance of integrating proteomics and transcriptomics data to gain a more complete understanding of cellular functions. The data suggest that the proteome is highly complete, with over 90% of the proteins within a factor of 60 of the median abundance. The study provides a comprehensive view of the proteome and transcriptome of a human cancer cell line, highlighting the importance of systems biology approaches in understanding cellular functions. The results demonstrate the potential of high-resolution MS and RNA-Seq in achieving a deep understanding of the proteome and transcriptome of a single cell type. The study also highlights the importance of integrating proteomics and transcriptomics data to gain a more complete understanding of cellular functions.A deep proteome and transcriptome mapping of a human cancer cell line, HeLa, was conducted using advanced mass spectrometry (MS) and RNA-Seq. The study identified 10,255 human proteins from 9,207 genes, with over 90% of the proteins having abundances within a factor of 60 of the median. RNA-Seq data revealed transcripts for nearly all detected proteins, with 11,936 protein-coding genes detected, including many low-abundance transcripts. The proteome and transcriptome data showed a high degree of correlation, with the proteome covering a large portion of the functional transcriptome. The study also demonstrated that the proteome was highly complete, with over 90% of the proteins within a factor of 60 of the median abundance. The data suggest that at least 10,000–12,000 genes are expressed in HeLa cells. The study provides a comprehensive view of the proteome and transcriptome of a human cancer cell line, highlighting the importance of systems biology approaches in understanding cellular functions. The results demonstrate the potential of high-resolution MS and RNA-Seq in achieving a deep understanding of the proteome and transcriptome of a single cell type. The study also highlights the importance of integrating proteomics and transcriptomics data to gain a more complete understanding of cellular functions. The data suggest that the proteome is highly complete, with over 90% of the proteins within a factor of 60 of the median abundance. The study provides a comprehensive view of the proteome and transcriptome of a human cancer cell line, highlighting the importance of systems biology approaches in understanding cellular functions. The results demonstrate the potential of high-resolution MS and RNA-Seq in achieving a deep understanding of the proteome and transcriptome of a single cell type. The study also highlights the importance of integrating proteomics and transcriptomics data to gain a more complete understanding of cellular functions.