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Quantitative Single-Cell Proteomics as a Tool to Characterize Cellular Hierarchies

https://doi.org/10.1101/745679
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Combined tissue and fluid proteomics with Tandem Mass Tags to identify low‐abundance protein biomarkers of disease in peripheral body fluid: An Alzheimer's Disease case study
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miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells
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The Proteogenomic Landscape of Curable Prostate Cancer
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Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors
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Not All Created Equal: Lineage Hard-Wiring in the Production of Blood
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A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade
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Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity
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Differences in Cell Cycle Status Underlie Transcriptional Heterogeneity in the HSC Compartment
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NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations
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Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing
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Evolution of the Cancer Stem Cell Model
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Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal
inferredcites →https://doi.org/10.1016/j.trecan.2018.02.003openalex-snapshot
Single-Cell Transcriptomic Analysis of Tumor Heterogeneity
inferredcites →https://doi.org/10.1021/acs.analchem.8b05399openalex-snapshot
Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry
inferredcites →https://doi.org/10.1021/acs.analchem.9b00327openalex-snapshot
Single Cell Proteomics by Data-Independent Acquisition To Study Embryonic Asymmetry in Xenopus laevis
inferredcites →https://doi.org/10.1021/acs.analchem.9b00345openalex-snapshot
Microsampling Capillary Electrophoresis Mass Spectrometry Enables Single-Cell Proteomics in Complex Tissues: Developing Cell Clones in Live Xenopus laevis and Zebrafish Embryos
inferredcites →https://doi.org/10.1021/acs.analchem.9b03349openalex-snapshot
High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labeling in a Nanodroplet Sample Preparation Platform
inferredcites →https://doi.org/10.1021/acs.analchem.9b04474openalex-snapshot
TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set
inferredcites →https://doi.org/10.1021/acs.jproteome.0c00675openalex-snapshot
Optimizing Accuracy and Depth of Protein Quantification in Experiments Using Isobaric Carriers
inferredcites →https://doi.org/10.1021/acs.jproteome.6b00745openalex-snapshot
Improvement of Quantitative Measurements in Multiplex Proteomics Using High-Field Asymmetric Waveform Spectrometry
inferredcites →https://doi.org/10.1021/pr050160fopenalex-snapshot
Development and Evaluation of a Micro- and Nanoscale Proteomic Sample Preparation Method
inferredcites →https://doi.org/10.1038/367645a0openalex-snapshot
A cell initiating human acute myeloid leukaemia after transplantation into SCID mice
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Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
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A 17-gene stemness score for rapid determination of risk in acute leukaemia
inferredcites →https://doi.org/10.1038/nature22993openalex-snapshot
Tracing the origins of relapse in acute myeloid leukaemia to stem cells
inferredcites →https://doi.org/10.1038/nature25193openalex-snapshot
A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies
inferredcites →https://doi.org/10.1038/nm.2415openalex-snapshot
Stem cell gene expression programs influence clinical outcome in human leukemia
inferredcites →https://doi.org/10.1038/nm0797-730openalex-snapshot
Human acute myeloid leukemia is organized as a hierarchy that originates from a primitive hematopoietic cell
inferredcites →https://doi.org/10.1038/nmeth.3971openalex-snapshot
Diffusion pseudotime robustly reconstructs lineage branching
inferredcites →https://doi.org/10.1038/nprot.2007.261openalex-snapshot
Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips
inferredcites →https://doi.org/10.1038/nrg3185openalex-snapshot
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
inferredcites →https://doi.org/10.1038/s41375-018-0227-5openalex-snapshot
The stem cell-associated gene expression signature allows risk stratification in pediatric acute myeloid leukemia
inferredcites →https://doi.org/10.1038/s41467-018-03367-wopenalex-snapshot
Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells
inferredcites →https://doi.org/10.1038/s41467-019-09078-0openalex-snapshot
SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells
inferredcites →https://doi.org/10.1038/s41570-020-0162-7openalex-snapshot
Single-cell analysis targeting the proteome
inferredcites →https://doi.org/10.1038/s41586-019-1367-0openalex-snapshot
Somatic mutations and cell identity linked by Genotyping of Transcriptomes
inferredcites →https://doi.org/10.1038/s41586-019-1652-yopenalex-snapshot
Decoding human fetal liver haematopoiesis
inferredcites →https://doi.org/10.1038/s41587-019-0113-3openalex-snapshot
Efficient integration of heterogeneous single-cell transcriptomes using Scanorama
inferredcites →https://doi.org/10.1038/s41592-020-01002-5openalex-snapshot
Defining the carrier proteome limit for single-cell proteomics
inferredcites →https://doi.org/10.1038/s41592-020-0781-4openalex-snapshot
TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples
inferredcites →https://doi.org/10.1038/s41598-019-41695-zopenalex-snapshot
From Louvain to Leiden: guaranteeing well-connected communities
inferredcites →https://doi.org/10.1039/d0sc03636fopenalex-snapshot
Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell
inferredcites →https://doi.org/10.1074/mcp.m115.056911openalex-snapshot
CONSTANd : A Normalization Method for Isobaric Labeled Spectra by Constrained Optimization
inferredcites →https://doi.org/10.1074/mcp.m116.065524openalex-snapshot
Extended Multiplexing of Tandem Mass Tags (TMT) Labeling Reveals Age and High Fat Diet Specific Proteome Changes in Mouse Epididymal Adipose Tissue
inferredcites →https://doi.org/10.1074/mcp.ra119.001857openalex-snapshot
An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics
inferredcites →https://doi.org/10.1091/mbc.e15-07-0499openalex-snapshot
Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency inSaccharomyces cerevisiae
inferredcites →https://doi.org/10.1093/bioinformatics/btv325openalex-snapshot
Diffusion maps for high-dimensional single-cell analysis of differentiation data
inferredcites →https://doi.org/10.1093/nar/gky1076openalex-snapshot
BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles
inferredcites →https://doi.org/10.1093/nar/gky1106openalex-snapshot
The PRIDE database and related tools and resources in 2019: improving support for quantification data
inferredcites →https://doi.org/10.1101/665307openalex-snapshot
Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity
inferredcites →https://doi.org/10.1101/gr.190595.115openalex-snapshot
Defining cell types and states with single-cell genomics
inferredcites →https://doi.org/10.1111/imr.12440openalex-snapshot
Granulopoiesis and granules of human neutrophils
inferredcites →https://doi.org/10.1126/science.1242379openalex-snapshot
Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures
inferredcites →https://doi.org/10.1126/science.aab2116openalex-snapshot
Distinct routes of lineage development reshape the human blood hierarchy across ontogeny
inferredcites →https://doi.org/10.1182/blood-2018-10-881441openalex-snapshot
A stemness screen reveals C3orf54/INKA1 as a promoter of human leukemia stem cell latency
inferredcites →https://doi.org/10.1186/s13059-017-1382-0openalex-snapshot
SCANPY: large-scale single-cell gene expression data analysis
inferredcites →https://doi.org/10.1186/s13059-018-1547-5openalex-snapshot
SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation
inferredcites →https://doi.org/10.1371/journal.pone.0098679openalex-snapshot
ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software
inferredcites →https://doi.org/10.21105/joss.00861openalex-snapshot
UMAP: Uniform Manifold Approximation and Projection
inferredcites →https://doi.org/10.7554/elife.50777openalex-snapshot
Single-cell proteomics reveals changes in expression during hair-cell development

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/ansa.202000152openalex-snapshot
The rise of single‐cell proteomics
inferred← citeshttps://doi.org/10.1007/978-1-0716-1024-4_27openalex-snapshot
Missing Value Monitoring to Address Missing Values in Quantitative Proteomics
inferred← citeshttps://doi.org/10.1007/978-1-0716-1936-0_6openalex-snapshot
Mass Spectrometry-Based Analytical Strategy for Single-Cell Proteomics
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Single-cell protein analysis by mass spectrometry
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Roadmap to functional characterization of the human intestinal microbiota in its interaction with the host
inferred← citeshttps://doi.org/10.1021/acs.analchem.1c04174openalex-snapshot
Quantitative Accuracy and Precision in Multiplexed Single-Cell Proteomics
inferred← citeshttps://doi.org/10.1021/acs.jproteome.0c00338openalex-snapshot
Addressing Cellular Heterogeneity in Cancer through Precision Proteomics
inferred← citeshttps://doi.org/10.1021/acs.jproteome.1c00670openalex-snapshot
Features of Peptide Fragmentation Spectra in Single-Cell Proteomics
inferred← citeshttps://doi.org/10.1038/s41467-022-29383-5openalex-snapshot
cyCombine allows for robust integration of single-cell cytometry datasets within and across technologies
inferred← citeshttps://doi.org/10.1038/s41592-020-01002-5openalex-snapshot
Defining the carrier proteome limit for single-cell proteomics
inferred← citeshttps://doi.org/10.1080/14789450.2020.1731309openalex-snapshot
Progress and pitfalls of using isobaric mass tags for proteome profiling
inferred← citeshttps://doi.org/10.1101/2021.04.14.439828openalex-snapshot
An automated workflow for multiplexed single-cell proteomics sample preparation at unprecedented sensitivity
inferred← citeshttps://doi.org/10.1101/2021.07.29.454362openalex-snapshot
Temporal variation in lymphocyte proteomics
inferred← citeshttps://doi.org/10.1101/665307openalex-snapshot
Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity
inferred← citeshttps://doi.org/10.1186/s13059-021-02267-5openalex-snapshot
Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2
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Artificial Intelligence to Decode Cancer Mechanism: Beyond Patient Stratification for Precision Oncology
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