PXD016573

PXD016573 is an original dataset announced via ProteomeXchange.

Title	Single Cell Proteomics and the Carrier Proteome Effect
Description	Single cell proteomics by mass spectrometry (SCoPE-MS) is a recently introduced method that utilizes isobaric labels to quantify multiplexed single cell proteomes. While this technique has generated great excitement, the technologies underlying SCoPE-MS - isobaric labels and mass spectrometry - comprise technical limitations with the potential to unfavorably impact data quality and biological interpretation. These limitations are due to the carrier proteome, a sample added at 25-500x single cell proteomes to enable peptide identifications. Here, we perform SCoPE-MS experiments with increasing amounts of carrier proteome and evaluate quantitative accuracy as it relates to mass analyzer dynamic range, multiplexing level, and number of ions sampled. We demonstrate that an increase in carrier proteome level requires a concomitant increase in the number of ions sampled to maintain quantitative accuracy – we term this the carrier proteome effect. Based on our findings, we provide guidance on experimental design, data collection, and data analysis to limit the impact of the carrier proteome effect within SCoPE-MS measurements.
HostingRepository	PRIDE
AnnounceDate	2020-12-16
AnnouncementXML	Submission_2020-12-15_22:28:41.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christopher Rose
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-12-04 03:28:12	ID requested
⏵ 1	2020-12-15 22:28:42	announced

Cheung TK, Lee CY, Bayer FP, McCoy A, Kuster B, Rose CM, Defining the carrier proteome limit for single-cell proteomics. Nat Methods, 18(1):76-83(2021) [pubmed]

submitter keyword: Human, LC-MSMS, Single Cell Proteomics

Christopher M. Rose
contact affiliation	Genentech, Inc.
contact email	rose.christopher@gene.com
lab head
Christopher Rose
contact affiliation	Genentech
contact email	Rose.Christopher@gene.com
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/2020/12/PXD016573

PRIDE project URI

• PRIDE
  1. PXD016573
     1. Label: PRIDE project
     2. Name: Single Cell Proteomics and the Carrier Proteome Effect