Integrative proteogenomics using ProteomeGenerator2 Journal Article
| Authors: | Kwok, N.; Aretz, Z.; Takao, S.; Ser, Z.; Cifani, P.; Kentsis, A. |
| Article Title: | Integrative proteogenomics using ProteomeGenerator2 |
| Abstract: | Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. Likewise, advances in mass spectrometry proteomics now permit highly sensitive and accurate studies of protein expression at the whole proteome-scale. However, most proteomic studies rely on consensus databases to match spectra to peptide and protein sequences, and thus remain limited to the analysis of canonical protein sequences. Here, we develop ProteomeGenerator2 (PG2), based on the scalable and modular ProteomeGenerator framework. PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as noncanonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. We benchmarked PG2 using synthetic data and genomic, transcriptomic, and proteomic analysis of human leukemia cells. PG2 can be integrated with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms, and is available open-source from https://github.com/kentsisresearchgroup/ProteomeGenerator2. © 2023 American Chemical Society. |
| Keywords: | mass spectrometry; peptide; proteomics; transcriptomics; peptides; genomics; procedures; humans; human; proteogenomics; comprehensive proteomics |
| Journal Title: | Journal of Proteome Research |
| Volume: | 22 |
| Issue: | 8 |
| ISSN: | 1535-3893 |
| Publisher: | American Chemical Society |
| Date Published: | 2023-08-04 |
| Start Page: | 2750 |
| End Page: | 2764 |
| Language: | English |
| DOI: | 10.1021/acs.jproteome.3c00005 |
| PUBMED: | 37418425 |
| PROVIDER: | scopus |
| PMCID: | PMC10783198 |
| DOI/URL: | |
| Notes: | Article -- MSK Cancer Center Support Grant (P30 CA0098748) acknowledged in PubMed and PDF -- MSK corresponding author is Alex Kentsis -- Source: Scopus |
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