PXD031171

PXD031171 is an original dataset announced via ProteomeXchange.

Title	iSPI: A Multi-dimensional, Regenerable, Proteome-scale, Human Phosphopeptide Resource for Phosphoproteomics
Description	Mass spectrometry-based phosphoproteomics has become indispensable for understanding cellular signaling in complex biological systems. Despite the central role of protein phosphorylation, the field still lacks inexpensive, regenerable, and diverse phosphopeptides with ground truth phosphorylation positions that can serve as gold standards for method development and pipeline evaluation. Here, we present Iterative Synthetically Phosphorylated Isomers (iSPI), a proteome-scale library of human-derived phosphoserine-containing phosphopeptides produced in E. coli using the phosphoserine orthogonal translation system. Because phosphoserine is genetically encoded, the position of phosphorylation is precisely known. Since the library is synthesized in E. coli, phosphopeptide production is scalable and regenerable. We demonstrate the utility of iSPI as a phosphopeptide standard to investigate instrument acquisition methods, to evaluate and optimize phosphorylation site localization algorithms, and to compare performance across data analysis pipelines. As a direct result of iSPI analyses, we present AscorePro, an updated version of the Ascore algorithm that has been specifically optimized for localization of phosphorylation sites in higher energy fragmentation spectra. In addition, we provide the FLR Viewer for Phosphorylation Site Localization, a browser-based tool allowing the community to calculate phosphorylation site false localization rates using their own workflows and analysis pipelines. Thus, iSPI and its associated data constitute a useful, multi-dimensional resource for the phosphoproteomics community.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:09:33.480.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Brandon Gassaway
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	O-phosphorylated residue; monohydroxylated residue; deamidated residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2022-01-22 09:48:07	ID requested
1	2022-10-26 07:11:47	announced
⏵ 2	2023-11-14 08:09:34	announced	2023-11-14: Updated project metadata.

Gassaway BM, Li J, Rad R, Mintseris J, Mohler K, Levy T, Aguiar M, Beausoleil SA, Paulo JA, Rinehart J, Huttlin EL, Gygi SP, A multi-purpose, regenerable, proteome-scale, human phosphoserine resource for phosphoproteomics. Nat Methods, 19(11):1371-1375(2022) [pubmed]

submitter keyword: FLR,Phosphoproteomics, Synthetic Biology

Steven Gygi
contact affiliation	Harvard University Medical School, Department of Cell Biology
contact email	steven_gygi@hms.harvard.edu
lab head
Brandon Gassaway
contact affiliation	Harvard Medical School
contact email	brandon_gassaway@hms.harvard.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/2022/10/PXD031171

PRIDE project URI

• PRIDE
  1. PXD031171
     1. Label: PRIDE project
     2. Name: iSPI: A Multi-dimensional, Regenerable, Proteome-scale, Human Phosphopeptide Resource for Phosphoproteomics