PXD011353-3

PXD011353 is an original dataset announced via ProteomeXchange.

Title	PROTEOFORMER 2.0: MS validation
Description	PROTEOFORMER is a pipeline for generating a search space of candidate translation products based on ribosome profiling data. The pipeline was published in 2014, but since then, several features have been added. For this project, the PROTEOFORMER pipeline 2.0 was tested on human HCT116 and Jurkat cell ribosome profiling data with all its new features and then compared to raw MS data of both cell lines, validating its use as a proteogenomic tool. In this study, results of 3 proteoform calling methods were combined (classical PROTEOFORMER proteoform calling, PRICE and SPECtre). Afterwards, results were eventually combined with the canonical or splicing-included version of human UniProt. The different described combinations were exported as a FASTA file and used as search space for searching matching MS data.
HostingRepository	PRIDE
AnnounceDate	2023-05-14
AnnouncementXML	Submission_2023-05-14_14:15:15.560.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	StevenVerbruggen
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-10-15 02:01:55	ID requested
1	2019-05-03 13:37:56	announced
2	2021-04-07 21:52:12	announced	2021-04-08: Updated publication reference for PubMed record(s): 31040227, 33823297.
⏵ 3	2023-05-14 14:15:17	announced	2023-05-14: Updated project metadata.
4	2024-10-22 04:49:40	announced	2024-10-22: Updated project metadata.

Verbruggen S, Ndah E, Van Criekinge W, Gessulat S, Kuster B, Wilhelm M, Van Damme P, Menschaert G, PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms. Mol Cell Proteomics, 18(8 suppl 1):S126-S140(2019) [pubmed]

Verbruggen S, Gessulat S, Gabriels R, Matsaroki A, Van de Voorde H, Kuster B, Degroeve S, Martens L, Van Criekinge W, Wilhelm M, Menschaert G, Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics. Mol Cell Proteomics, 20():100076(2021) [pubmed]

ProteomeXchange project tag: EPIC-XS

submitter keyword: Jurkat, PROTEOFORMER,HCT116, MSMS

GerbenMenschaert
contact affiliation	BioBix, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, Belgium
contact email	Gerben.Menschaert@UGent.be
lab head
StevenVerbruggen
contact affiliation	BioBix
contact email	Steven.Verbruggen@UGent.be
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/2019/05/PXD011353

PRIDE project URI

• PRIDE
  1. PXD011353
     1. Label: PRIDE project
     2. Name: PROTEOFORMER 2.0: MS validation