PXD012255

PXD012255 is an original dataset announced via ProteomeXchange.

Title	Phosphoproteomics using CZE-MS/MS
Description	Phosphoproteomics requires better separation of phosphopeptides to boost the coverage of the phosphoproteome. We argue that an alternative separation method that produces orthogonal phosphopeptide separation to the widely used LC needs to be considered. Capillary zone electrophoresis (CZE) is one important alternative because CZE and LC are orthogonal for phosphopeptide separation and because the migration time of peptides in CZE can be accurately predicted. In this work, we coupled strong cation exchange (SCX)-reversed-phase LC (RPLC) to CZE-MS/MS for large-scale phosphoproteomics of the colon carcinoma HCT116 cell line. The CZE-MS/MS-based platform identified 11,555 phosphopeptides. The phosphopeptide dataset is at least 100% larger than that from previous CZE-MS/MS studies and will be a valuable resource for building a model for predicting the migration time of phosphopeptides in CZE. Preliminary investigations demonstrated that predicted and observed electrophoretic mobility of phosphopeptides containing one phosphoryl group had good linear correlations (R2≥0.94). Adding one phosphoryl group on a peptide decreased its electrophoretic mobility dramatically because the phosphoryl group reduced the peptide’s charge by roughly 1 based on our experimental data. Phosphopeptides tended to migrate significantly slower than unphosphopeptides in the CZE separation capillary and phosphorylated and unphosphorylated forms of peptides were separated well by CZE. The CZE-MS/MS and LC-MS/MS were complementary in large-scale phosphopeptide identifications and produced different phosphosite motifs from the HCT116 cell line. The data highlight the value of CZE-MS/MS for phosphoproteomics as a complementary separation approach for not only improving the phosphoproteome coverage but also providing more insight into the phosphosite motifs.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:51:50.411.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Liangliang Sun
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-01-08 00:12:27	ID requested
1	2019-01-16 00:42:47	announced
⏵ 2	2024-10-22 04:51:58	announced	2024-10-22: Updated project metadata.

10.1021/acs.analchem.8b04770;

Chen D, Ludwig KR, Krokhin OV, Spicer V, Yang Z, Shen X, Hummon AB, Sun L, Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Large-Scale Phosphoproteomics with the Production of over 11,000 Phosphopeptides from the Colon Carcinoma HCT116 Cell Line. Anal Chem, 91(3):2201-2208(2019) [pubmed]

curator keyword: Biological

submitter keyword: cze-ms/ms, HCT116 cell line, PHOSPHOPROTEOMICS

Liangliang Sun
contact affiliation	Department of Chemistry, Michigan State University
contact email	lsun@chemistry.msu.edu
lab head
Liangliang Sun
contact affiliation	Michigan State University
contact email	lsun@chemistry.msu.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/2019/01/PXD012255

PRIDE project URI

• PRIDE
  1. PXD012255
     1. Label: PRIDE project
     2. Name: Phosphoproteomics using CZE-MS/MS