PXD037058

PXD037058 is an original dataset announced via ProteomeXchange.

Title	HyPep: An Open-Source Software for Identification and Discovery of Neuropeptides using Sequence Homology Searching
Description	Neuropeptides are a class of endogenous peptides that have key regulatory roles in biochemical, physiological, and behavioral processes. Mass spectrometry analyses of neuropeptides often rely on protein informatics tools for database searching and peptide identification. As neuropeptide databases are typically experimentally built and comprised of short sequences with high sequence similarity to each other, we developed a novel database searching tool, HyPep, which utilizes sequence homology searching for peptide identification. HyPep aligns database-free, de novo sequenced peptide sequences generated through PEAKS software with neuropeptide database sequences to identify neuropeptides based on an alignment score. HyPep performance was optimized using LC-MS/MS measurements of peptide extracts from various C. sapidus neuronal tissue types and compared with a commercial database searching software, PEAKS DB. HyPep identified more neuropeptides from each tissue type than PEAKS DB at 1% false discovery rate and the false match rate from both programs was 2%. In addition to identification, this report describes how HyPep can aid in the discovery of novel neuropeptides.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:28:34.918.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nhu Vu
SpeciesList	scientific name: Drosophila melanogaster (Fruit fly); NCBI TaxID: 7227;
ModificationList	amidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-28 00:59:31	ID requested
1	2023-02-02 06:01:51	announced
⏵ 2	2023-11-14 07:28:38	announced	2023-11-14: Updated project metadata.

Vu NQ, Yen HC, Fields L, Cao W, Li L, HyPep: An Open-Source Software for Identification and Discovery of Neuropeptides Using Sequence Homology Search. J Proteome Res, 22(2):420-431(2023) [pubmed]

submitter keyword: peptidomics, HyPep, homology, mass spectrometry, peptide, de novo sequencing, FDR,Neuropeptide

Lingjun Li
contact affiliation	Professor Vilas Distinguished Achievement Professor of Pharmaceutical Sciences and Chemistry Charles Melbourne Johnson Distinguished Chair in Pharmaceutical Sciences
contact email	lingjun.li@wisc.edu
lab head
Nhu Vu
contact affiliation	University of Wisconsin-Madison
contact email	nqvu@wisc.edu
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/2023/02/PXD037058

PRIDE project URI

• PRIDE
  1. PXD037058
     1. Label: PRIDE project
     2. Name: HyPep: An Open-Source Software for Identification and Discovery of Neuropeptides using Sequence Homology Searching