PXD048595

PXD048595 is an original dataset announced via ProteomeXchange.

Title	Quantification Quality Control Emerges as A Crucial Factor to Enhance Single Cell Proteomics Data Analysis
Description	Mass spectrometry (MS)-based single-cell proteomics (SCP) provides us the opportunity to unbiasedly explore biological variability within cells without the limitation of antibody availability. This field is rapidly developed with the main focuses on instrument advancement, sample preparation refinement, and signal boosting methods; however, the optimal data processing and analysis are rarely investigated which holds an arduous challenge because of the high proportion of missing values and batch effect. Here, we introduced a quantification quality control to intensify the identification of differentially expressed proteins (DEPs) by considering both within and across SCP data. Combining quantification quality control with isobaric match between runs (IMBR) and PSM-level normalization, an additional 12% and 19% of proteins and peptides, regarding to more than 90% of proteins/peptides contained valid value, were quantified. Clearly, quantification quality control was able to reduce quantification variations and q-values with the more apparent cell type separations. In addition, we found that PSM-level normalization performed similarly to other protein level normalization but kept the original data profiles without the additional requirement of data manipulation. In proof of concept of our refined pipeline, six uniquely identified DEPs exhibiting varied fold-changes and playing critical roles for melanoma and monocyte functionalities were selected for validation using immunoblotting. Five out of six validated DEPs showed an identical trend with the SCP dataset, emphasizing the feasibility of combining the IMBR, cell quality control, and PSM-level normalization in SCP analysis, which is beneficial for future SCP studies.
HostingRepository	jPOST
AnnounceDate	2025-01-09
AnnouncementXML	Submission_2025-01-08_21:26:10.730.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Miao-Hsia Lin
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue; L-methionine sulfoxide
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-16 02:13:19	ID requested
⏵ 1	2025-01-08 21:26:11	announced

Yu SH, Chen SC, Wu PS, Kuo PI, Chen TA, Lee HY, Lin MH, Quantification Quality Control Emerges as a Crucial Factor to Enhance Single-Cell Proteomics Data Analysis. Mol Cell Proteomics, 23(5):100768(2024) [pubmed]

submitter keyword: Single-cell proteomics

isobaric labeling

matching between runs

PSM-level normalization

differential expression analysis

Miao-Hsia Lin
lab head
Miao-Hsia Lin
contact affiliation	Department of Microbiology, College of Medicine, National Taiwan University
dataset submitter

jPOST dataset URI

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