PXD048926

PXD048926 is an original dataset announced via ProteomeXchange.

Title	Increasing Proteome Coverage Through a Reduction in Analyte Complexity and Its Applications for Single-Cell Proteomics
Description	The advancement of sophisticated instrumentation in mass spectrometry has catalyzed a more in-depth exploration of complex proteomes. This exploration necessitates a nuanced balance in experimental design, particularly between quantitative precision and the enumeration of analytes detected. In bottom-up proteomics, a key challenge is that the oversampling of abundant proteins can adversely affect the identification of a diverse array of unique proteins. This issue is especially pronounced in samples with a limited quantity of analytes, such as small tissue biopsies or single-cell samples. Methods such as depletion/fractionation are not optimal to reduce oversampling in single cell samples, and other improvements on LC and mass spectrometry technology and methods have been developed to address the trade-off between precision and enumeration. We demonstrate that by using a mono-substrate protease for proteomic analysis of samples with low analyte concentrations, an improvement in proteome coverage can be achieved, while maintaining similar quantitative accuracy established by trypsin. This improvement is particularly vital for single-cell samples, where the limited number of protein copies, especially in the context of low-abundance proteins, poses a substantial challenge.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:50:33.860.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Marion Pang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-26 14:06:19	ID requested
1	2024-07-16 18:48:17	announced
⏵ 2	2024-10-22 06:50:34	announced	2024-10-22: Updated project metadata.

10.1021/ACS.JPROTEOME.4C00062;

submitter keyword: Mass Spectrometry, Analyte Complexity, Proteomics

Tsui-Fen Chou
contact affiliation	Proteome Exploration Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
contact email	tfchou@caltech.edu
lab head
Marion Pang
contact affiliation	California Institute of Technology
contact email	marion.pang@caltech.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/2024/07/PXD048926

PRIDE project URI

• PRIDE
  1. PXD048926
     1. Label: PRIDE project
     2. Name: Increasing Proteome Coverage Through a Reduction in Analyte Complexity and Its Applications for Single-Cell Proteomics