ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR968/001/SRR9685281/SRR9685281_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR968/001/SRR9685281/SRR9685281_1.fastq.gzprimaryOK200GenomicsIMB Mainzhttps://www.ebi.ac.uk/ena/browser/view/PRJNA554660By proteotranscriptomics, combining in-depth transcriptome sequencing and high resolution mass spectrometry, we establish protein evidence for more than 6000 genes. Our approach shows a precision rate of 96% in terms of annotated and detected protein-coding genes. We additionally experimentally classify the localization of several thousand proteins using the recently published LOPIT-DC workflow⁠ providing not only accurate gene models for the protein-coding genes, but also the subcellular localization of their proteins by spatial proteomics. Overall, we provide herea proof of concept for the generation of species-, strain- and cell-line-specific gene annotation for protein-coding genes based on experimental evidence without the need of a sequenced genome.ENAfalseProteotranscriptomics assisted gene annotation of Bombyx mori2023-05-192020-08-15PRJNA554660