PXD017626

PXD017626 is an original dataset announced via ProteomeXchange.

Title	An improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) strategy for precise quantitative single-cell proteomics
Description	Mass spectrometry (MS)-based proteomics has great potential for overcoming the limitations of antibody-based immunoassays for antibody-independent, comprehensive, and quantitative proteomic analysis of single cells. Indeed, recent advances in nanoscale sample preparation have enabled effective processing of single cells. In particular, the concept of using boosting/carrier channels in isobaric labeling to increase the sensitivity in MS detection has also been increasingly used for quantitative proteomic analysis of small-sized samples including single cells. However, the full potential of such boosting/carrier approaches has not been significantly explored, nor has the resulting quantitation quality been carefully evaluated. Herein, we have further evaluated and optimized our recent boosting to amplify signal with isobaric labeling (BASIL) approach, originally developed for quantifying phosphorylation in small number of cells, for highly effective analysis of proteins in single cells. This improved BASIL (iBASIL) approach enables reliable quantitative single-cell proteomics analysis with greater proteome coverage by carefully controlling the boosting-to-sample ratio (e.g., in general <100x) and optimizing MS automatic gain control (AGC) and ion injection time settings in MS/MS analysis (e.g., 5E5 and 300 ms, respectively, which is significantly higher than that used in typical bulk analysis). Using standard LC-MS platforms, iBASIL enabled identification of ~2,500 proteins and precise quantification of ~1,500 proteins in the analysis of 104 FACS-isolated single cells, with the resulting protein profiles robustly clustering the cells from three different acute myeloid leukemia cell lines. This study highlights the importance of carefully evaluating and optimizing the boosting and MS data acquisition conditions for achieving robust, comprehensive proteomic analysis of single cells.
HostingRepository	jPOST
AnnounceDate	2020-03-05
AnnouncementXML	Submission_2022-09-18_02:29:19.764.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chia-Feng Tsai
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide; unknown modification; unknown modification; alpha-amino acetylated residue
Instrument	Q Exactive; LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2020-02-19 15:31:16	ID requested
1	2020-03-05 10:36:10	announced
2	2021-02-04 17:05:40	announced	2021-02-04: Updated FTP location.
⏵ 3	2022-09-18 02:29:20	announced	2022-09-18: Updated FTP location.

Tsai CF, Zhao R, Williams SM, Moore RJ, Schultz K, Chrisler WB, Pasa-Tolic L, Rodland KD, Smith RD, Shi T, Zhu Y, Liu T, An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics. Mol Cell Proteomics, 19(5):828-838(2020) [pubmed]

submitter keyword: boosting ratio, automatic gain control (AGC), iBASIL, ion injection time (IT), single-cell proteomics

Tao Liu
lab head
Chia-Feng Tsai
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/JPST000723/