PXD027135

PXD027135 is an original dataset announced via ProteomeXchange.

Title	Nanoparticle-aided nanoreactor for large-scale proteomics of few mammalian cells
Description	Large-scale bottom-up proteomics of few even single cells is crucial for a better understanding of the roles played by cell-to-cell heterogeneity in disease and development. Novel proteomic methodologies with extremely high sensitivity are required for few even single-cell proteomics. Sample processing with high recovery and no contaminants is one key step. Here we developed a nanoparticle-aided nanoreactor for nanoproteomics (Nano3) technique for processing low-nanograms of mammalian cell proteins for large-scale proteome profiling. The Nano3 technique employed nanoparticles packed in a capillary channel to form a nanoreactor (≤30 nL) for concentrating, cleaning, and digesting proteins originally in a lysis buffer containing sodium dodecyl sulfate (SDS), followed by nanoRPLC-MS/MS analysis. The Nano3 method identified a 40-times higher number of proteins based on MS/MS from 2-ng mouse brain protein samples compared to the SP3 (Single-Pot Solid-Phase-enhanced Sample Preparation) method, which performed the sample processing using the nanoparticles in a 10-µL solution in an Eppendorf tube. The data indicates a drastically higher sample recovery of the Nano3 compared to the SP3 method for processing mass-limited proteome samples. In this pilot study, the Nano3 method was further applied in processing 10-1000 HeLa cells for bottom-up proteomics, producing 444 ± 263 (n=4) (MS/MS) and 987 ± 292 (n=4) [match between runs (MBR)+MS/MS] protein identifications from only 10 HeLa cells using a Q-Exactive HF mass spectrometer. The preliminary results render the Nano3 method a useful approach for processing few mammalian cells for large-scale proteome profiling.
HostingRepository	PRIDE
AnnounceDate	2022-07-11
AnnouncementXML	Submission_2022-07-11_08:42:35.835.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	2021-07-07 00:40:59	ID requested
⏵ 1	2022-07-11 08:42:36	announced

Yang Z, Zhang Z, Chen D, Xu T, Wang Y, Sun L, Nanoparticle-Aided Nanoreactor for Nanoproteomics. Anal Chem, 93(30):10568-10576(2021) [pubmed]

submitter keyword: nanoparticle, nanoreactor, nanoproteomics, single-cell proteomics, few-cell proteomics, mass-limited sample, bottom-up proteomics

Liangliang Sun
contact affiliation	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/2022/07/PXD027135

PRIDE project URI

• PRIDE
  1. PXD027135
     1. Label: PRIDE project
     2. Name: Nanoparticle-aided nanoreactor for large-scale proteomics of few mammalian cells