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PXD016573 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleSingle Cell Proteomics and the Carrier Proteome Effect
DescriptionSingle 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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterChristopher Rose
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListTMT6plex-126 reporter+balance reagent acylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02019-12-04 03:28:12ID requested
12020-12-15 22:28:42announced
Publication List
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]
Keyword List
submitter keyword: Human, LC-MSMS, Single Cell Proteomics
Contact List
Christopher M. Rose
contact affiliationGenentech, Inc.
contact emailrose.christopher@gene.com
lab head
Christopher Rose
contact affiliationGenentech
contact emailRose.Christopher@gene.com
dataset submitter
Full Dataset Link List
Dataset FTP location
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