MassIVE MSV000085959

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Single Cell Proteomics and the Carrier Proteome Effect

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Description

Single cell proteomics by mass spectrometry (SCoPE-MS) is a recently introduced method to quantify multiplexed single cell proteomes. While this technique has generated great excitement, the underlying technologies (isobaric labeling and mass spectrometry) comprise technical limitations with the potential to effect data quality and biological interpretation. These limitations are particularly relevant when a carrier proteome, a sample added at 25-500x single cell proteomes, is used to enable peptide identifications. Here, we perform controlled experiments with increasing carrier proteome amounts 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. Lastly, we introduce Single Cell Proteomics Companion a program that enables rapid evaluation of single cell proteomics data and recommends instrument and data analysis parameters for improved data quality. [doi:10.25345/C5KT83] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Single Cell Proteomics ; TMT ; Quantitative Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Christopher Rose, Genentech, United States
Submitting User: CMRose5
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Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

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Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
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