Dataset Information

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 proteome-scale. However, most proteomic studies remain limited to the analysis of canonical reference proteomes. 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 non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Leukocyte, Cell Culture

DISEASE(S): Acute Leukemia

SUBMITTER: Alex Kentsis

LAB HEAD: Alex Kentsis

PROVIDER: PXD037061 | Pride | 2024-05-22

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	DB_search_psm.csv	Csv
	MS205706QEHF_Alex_Kentsis_Kasumi1_G01.raw	Raw
	MS205706QEHF_Alex_Kentsis_Kasumi1_G02.raw	Raw
	MS205706QEHF_Alex_Kentsis_Kasumi1_G03.raw	Raw
	MS205706QEHF_Alex_Kentsis_Kasumi1_G04.raw	Raw

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Publications

Integrative Proteogenomics Using ProteomeGenerator2.

Kwok Nathaniel N Aretz Zita Z Takao Sumiko S Ser Zheng Z Cifani Paolo P Kentsis Alex A

Journal of proteome research 20230707 8

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 t ...[more]

PMID: 37418425

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