PXD047627

PXD047627 is an original dataset announced via ProteomeXchange.

Title	Solid phase microextraction-aided capillary zone electrophoresis-mass spectrometry: ready for bottom-up proteomics of single human cells
Description	Capillary zone electrophoresis-mass spectrometry (CZE-MS) has been recognized as a valuable technique for proteomics of mass-limited biological samples (i.e., single cells) due to its high efficiency and high sensitivity for peptide separation and detection. However, its broad adoption for single cell proteomics (SCP) of human cells has been impeded by the low sample loading capacity of CZE, only allowing to use less than 5% of the available peptide material for measurements. Here we present a reversed-phase based solid phase microextraction (RP-SPME)-CZE-MS platform to solve the low sample loading capacity issue of CZE, paving the way for SCP of human cells using CZE-MS. The RP-SPME-CZE system was constructed in one fused silica capillary with zero dead volume for connection via in-situ synthesis of a frit, followed by packing C8 beads into the capillary to form a roughly 2-mm-long SPME section. Peptides were captured by SPME, and then eluted with a buffer containing 30%(v/v) acetonitrile and 50 mM ammonium acetate (pH 6.5), followed by dynamic pH junction-based CZE-MS. The SPME-CZE-MS enabled the injection of nearly 40% of the available peptide sample for measurements. The system identified 257 ± 24 proteins and 523 ± 69 peptides (N=2) when only 0.25 ng of a commercial HeLa cell digest was available in the sample vial and 0.1 ng of the sample was injected. The available peptide amount is equivalent to the protein mass of two HeLa cells. The data indicates that SPME-CZE-MS offers sufficient sensitivity for SCP of human cells.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:37:55.532.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	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-07 14:15:01	ID requested
1	2024-05-01 13:40:19	announced
⏵ 2	2024-10-22 06:37:56	announced	2024-10-22: Updated project metadata.

Col, ó, n Rosado JA, Sun L, Solid-Phase Microextraction-Aided Capillary Zone Electrophoresis-Mass Spectrometry: Toward Bottom-Up Proteomics of Single Human Cells. J Am Soc Mass Spectrom, 35(6):1120-1127(2024) [pubmed]

10.1021/jasms.3c00429;

submitter keyword: HeLa, Single cell proteomics, mass limited, Solid phase microextraction, mass spectrometry, Bottom-up proteomics

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/2024/05/PXD047627

PRIDE project URI

• PRIDE
  1. PXD047627
     1. Label: PRIDE project
     2. Name: Solid phase microextraction-aided capillary zone electrophoresis-mass spectrometry: ready for bottom-up proteomics of single human cells