ProteomeGenerator analysis of K052

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UID: 11091

Author(s): Kentsis, Alex* * MSK affiliated

Description: To improve identification of canonical and non-canonical protein isoforms, we introduced ProteomeGenerator, a framework for reference-guided and de novo proteogenomic database generation from transcriptomic sequencing dataset. The proteomic databases output by ProteomeGenerator contain only proteins encoded by actively transcribed genes, and includes sample-specific protein isoforms resulting from non-canonical transcription and mRNA editing. We applied this workflow to the proteogenomic analysis of spliceosome-defective K052 SRSF2(P95H) cells, demonstrating high-confidence identification of proteins isoforms arising from intron inclusion and non-canonical splicing, as well as improved overall estimation of false-discovery rate from the focused database assembled by ProteomeGenerator.

Subject of Study

Subject(s)

Access via PRIDE

Accession #: PXD008381
Access Restrictions: Free to All
Access Instructions: All public datasets available in PRIDE Archive in the repository can be accessed via the website by FTP link, Web Service (for programmatic access), and the PRIDE Inspector stand-alone tool.
Associated Publications: Cifani P, Dhabaria A, Chen Z, Yoshimi A, Kawaler E, Abdel-Wahab O, Poirier J, Kentsis A. ProteomeGenerator: A framework for comprehensive proteomics based on de novo transcriptome assembly and high-accuracy peptide mass spectral matching. Journal of Proteome Research. 2018; 17(11):3681-3692.
Equipment Used: Orbitrap Fusion Lumos
Software Used: Peaks
a software platform with complete solutions for discovery proteomics, including protein identification and quantification, analysis of post-translational modifications (PTMs) and sequence variants (mutations), and peptide/protein de novo sequencing
Dataset Format(s): CSV, RAW
Dataset Size: 105.6 GB

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