PXD019626

PXD019626 is an original dataset announced via ProteomeXchange.

Title	Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics
Description	Large numbers of cells are generally required for quantitative global proteome profiling due to the significant surface adsorption losses associated with sample processing. Such bulk measurement obscures important cell-to-cell variability (cell heterogeneity) and makes proteomic profiling impossible for rare cell populations (e.g., circulating tumor cells (CTCs)). Here we report a surfactant-assisted one-pot sample preparation coupled with mass spectrometry (MS) termed SOP-MS for label-free global single-cell proteomics. SOP-MS capitalizes on the combination of a MS-compatible nonionic surfactant, n-Dodecyl-β-D-maltoside, and hydrophobic surface-based low-bind tubes or multi-well plates for ‘all-in-one’ one-pot sample preparation. This ‘all-in-one’ method including elimination of all sample transfer steps maximally reduces surface adsorption losses by ≥20-fold for effective processing of single cells, thus significantly improving detection sensitivity for single-cell proteomics. This method allows for the first time, convenient, label-free quantification of hundreds of proteins from single human cells and ~1200 proteins from small tissue sections (close to ~20 cells). When applied to a patient CTC-derived xenograft (PCDX) model at the single-cell resolution, SOP-MS can reveal distinct protein signatures between primary tumor cells and early metastatic lung cells, which are related to the selection pressure of anti-tumor immunity during breast cancer metastasis. The approach paves the way for routine, precise, quantitative single-cell proteomics.
HostingRepository	jPOST
AnnounceDate	2020-11-24
AnnouncementXML	Submission_2022-09-18_03:33:08.079.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tujin Shi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxymethyl-L-cysteine; L-methionine sulfoxide
Instrument	Q Exactive; LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-07 07:31:55	ID requested
1	2020-11-24 00:23:33	announced
2	2021-02-04 16:52:01	announced	2021-02-04: Updated FTP location.
⏵ 3	2022-09-18 03:33:08	announced	2022-09-18: Updated FTP location.

Dataset with its publication pending

submitter keyword: Surfactant-assisted one-pot sample preparation coupled with MS (SOP-MS), single-cell proteomics, nonionic surfactant, single cells, patient CTC-derived xenograft (PCDX)

Tujin Shi
lab head
Tujin Shi
contact affiliation	Pacific Northwest National Laboratory
dataset submitter

jPOST dataset URI

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.jpostdb.org/JPST000866/