We performed a comprehensive integrative analyses of mass spectrometry-based proteomics and transcriptomic sequencing data from greater than 900 patients across nine cancer types. This enabled us to identify 19,871 novel peptides derived from 8,903 long noncoding RNAs (lncRNAs). We also exploited open reading frames overlapping the backspliced region of circular RNAs (circRNAs) to identify 3,238 peptides that are uniquely derived from 2,834 circRNAs and not their corresponding linear RNAs. We hope this pan-cancer proteogenomic analysis will serve as a resource for evaluating the coding potential of lncRNAs and circRNAs that could aid future mechanistic studies exploring their function in cancer. Please use this website, PepTransDB (Peptides in Transcripts Database), to explore the results or download the data.