PXD037061-1

PXD037061 is an original dataset announced via ProteomeXchange.

Title	Integrative proteogenomics using ProteomeGenerator2
Description	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.
HostingRepository	PRIDE
AnnounceDate	2024-05-22
AnnouncementXML	Submission_2024-05-22_05:37:35.390.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alex Kentsis
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-28 01:00:44	ID requested
⏵ 1	2024-05-22 05:37:36	announced
2	2024-10-22 06:41:21	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.3c00005;

Kwok N, Aretz Z, Takao S, Ser Z, Cifani P, Kentsis A, Integrative Proteogenomics Using ProteomeGenerator2. J Proteome Res, 22(8):2750-2764(2023) [pubmed]

submitter keyword: Proteogenomics, genomics, transcriptomics, comprehensive proteomics

Alex Kentsis
contact affiliation	Molecular Pharmacology Program, Sloan Kettering Institute, Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, and Doctor of Medicine Program, Weill Cornell Medicine
contact email	kentsisresearchgroup@gmail.com
lab head
Alex Kentsis
contact affiliation	Memorial Sloan Kettering Cancer Center
contact email	kentsisresearchgroup@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/05/PXD037061

PRIDE project URI

• PRIDE
  1. PXD037061
     1. Label: PRIDE project
     2. Name: Integrative proteogenomics using ProteomeGenerator2