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. 2022 Mar 3;23:69. doi: 10.1186/s13059-022-02624-y

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© The Author(s) 2022

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 6 — Long-read-informed protein isoform detection. a Scenarios in which long-read transcriptomic abundance values can be used to “rescue and resolve” protein group identifications for improved protein isoform detection. Note that peptide locations are not drawn to scale. See Ref. [10] for original cases. b The number of protein groups containing PacBio-derived protein isoforms identified in a traditional (normal) search versus one that incorporates long-read RNA-seq data to rescue isoforms (Rescue & Resolve algorithm). c Example of two rescued isoforms from the gene IFI16. PB.1137.5 and PB.1137.24 both have high transcriptional abundance and contain novel exon skipping events, but both lack unique sequence regions containing an identified peptide. CPM, full-length copies per million reads. d, e The percent of rescued (d) and resolved or removed (e) protein isoforms validated compared to the derived null distribution from randomly rescued isoforms