Explanipedia

Limiting the impact of protein leakage in single-cell proteomics Open

Andrew Leduc, Yanxin Xu, Gergana Shipkovenska, Zhixun Dou, Nikolai Slavov · 2025

Limiting artifacts during sample preparation can significantly increase data quality in single-cell proteomics experiments. Towards this goal, we characterize the impact of protein leakage by analyzing thousands of primary single cells fro…

Impact of protein degradation and cell growth on mammalian proteomes Open

Andrew Leduc, Nikolai Slavov · 2025

Cellular protein concentrations are controlled by rates of synthesis and clearance, the lat-ter including protein degradation and dilution due to growth. Thus, cell growth rate may influence the mechanisms controlling variation in protein …

Inferring post-transcriptional regulation within and across cell types in human testis Open

Saad Khan, Megan Elcheikhali, Andrew Leduc, R. Gray Huffman, Jason Derks , et al. · 2024

Single-cell tissue atlases commonly use RNA abundances as surrogates for protein abundances. Yet, protein abundance also depends on the regulation of protein synthesis and degradation rates. To estimate the contributions of such post trans…

Alternate RNA decoding results in stable and abundant proteins in mammals Open

Shira Tsour, Rainer Machné, Andrew Leduc, S. Widmer, Jérémy Guez , et al. · 2024

Amino acid substitutions may substantially alter protein stability and function, but the contribution of substitutions arising from alternate translation (deviations from the genetic code) is unknown. To explore it, we analyzed deep proteo…

Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP Open

Andrew Leduc, Luke Khoury, Joshua Cantlon, Saad Khan, Nikolai Slavov · 2024

Limiting the impact of protein leakage in single-cell proteomics Open

Andrew Leduc, Yanxin Xu, Gergana Shipkovenska, Zhixun Dou, Nikolai Slavov · 2024

Limiting artifacts during sample preparation can significantly increase data quality in single-cell proteomics experiments. Towards this goal, we characterize the impact of protein leakage by analyzing thousands of primary single cells tha…

Single-nucleus proteomics identifies regulators of protein transport Open

Jason Derks, Tobias Jonson, Andrew Leduc, Saad Khan, Luke Khoury , et al. · 2024

The physiological response of a cell to stimulation depends on its proteome configuration. Therefore, the abundance variation of regulatory proteins across unstimulated single cells can be associatively linked with their response to stimul…

Massively paralleled droplet sample preparation for single cell proteomics facilitates analysis of complex samples Open

Andrew Leduc · 2024

Massively parallel sample preparation for multiplexed single-cell proteomics using nPOP Open

Andrew Leduc, Luke Koury, Joshua Cantlon, Nikolai Slavov · 2023

Single-cell proteomics by mass spectrometry (MS) allows quantifying proteins with high specificity and sensitivity. To increase its throughput, we developed nPOP, a method for parallel preparation of thousands of single cells in nanoliter …

Modeling and interpretation of single-cell proteogenomic data. Open

Andrew Leduc, Hannah Harens, Nikolai Slavov · 2023

Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable d…

Data-Driven Optimization of DIA Mass Spectrometry by DO-MS Open

Georg Wallmann, Andrew Leduc, Nikolai Slavov · 2023

Mass spectrometry (MS) enables specific and accurate quantification of proteins with ever-increasing throughput and sensitivity. Maximizing this potential of MS requires optimizing data acquisition parameters and performing efficient quali…

Modeling and interpretation of single-cell proteogenomic data Open

Andrew Leduc, Hannah Harens, Nikolai Slavov · 2023

Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable d…

An adult clock regulator links circadian rhythms to pancreatic β-cell maturation Open

Ana P. Montalvo, Zoe L. Gruskin, Andrew Leduc, Mai Liu, Zihan Gao , et al. · 2023

SUMMARY The circadian clock attunes metabolism to daily energy cycles, but how it regulates maturation of metabolic tissues is poorly understood. Here we show that DEC1, a clock transcription factor induced in adult islet β cells, coordina…

Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics Open

R. Gray Huffman, Andrew Leduc, Christoph Wichmann, Marco Di Gioia, Francesco Borriello , et al. · 2023

Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments Open

Laurent Gatto, Ruedi Aebersold, Jüergen Cox, Vadim Demichev, Jason Derks , et al. · 2023

Data-Driven Optimization of DIA Mass Spectrometry by DO-MS Open

Georg Wallmann, Andrew Leduc, Nikolai Slavov · 2023

Mass spectrometry (MS) enables specific and accurate quantification of proteins with ever increasing throughput and sensitivity. Maximizing this potential of MS requires optimizing data acquisition parameters and performing efficient quali…

pSCoPE: Prioritized Single-Cell Proteomics (data for generating publication figures) Open

R. Gray Huffman, Andrew Leduc, Christoph Wichmann, Marco Di Gioia, Francesco Borriello , et al. · 2022

Major aims of single-cell proteomics include increasing the consistency, sensitivity, and depth of protein quantification, especially for proteins and modifications of biological interest. To simultaneously advance all these aims, we devel…

pSCoPE: Prioritized Single-Cell Proteomics (data for generating publication figures) Open

R. Gray Huffman, Andrew Leduc, Christoph Wichmann, Marco Di Gioia, Francesco Borriello , et al. · 2022

Major aims of single-cell proteomics include increasing the consistency, sensitivity, and depth of protein quantification, especially for proteins and modifications of biological interest. To simultaneously advance all these aims, we devel…

pSCoPE: Prioritized Single-Cell Proteomics (data for generating publication figures) Open

R. Gray Huffman, Andrew Leduc, Christoph Wichmann, Marco Di Gioia, Francesco Borriello , et al. · 2022

Major aims of single-cell proteomics include increasing the consistency, sensitivity, and depth of protein quantification, especially for proteins and modifications of biological interest. To simultaneously advance all these aims, we devel…

Exploring functional protein covariation across single cells using nPOP Open

Andrew Leduc, R. Gray Huffman, Joshua Cantlon, Saad Khan, Nikolai Slavov · 2022

Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments Open

Laurent Gatto, Ruedi Aebersold, Jüergen Cox, Vadim Demichev, Jason Derks , et al. · 2022

Analyzing proteins from single cells by tandem mass spectrometry (MS) has become technically feasible. While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells, the accuracy and re…

Increasing the throughput of sensitive proteomics by plexDIA Open

Jason Derks, Andrew Leduc, Georg Wallmann, R. Gray Huffman, Matthew Willetts , et al. · 2022

Highly Parallel Droplet Sample Preparation for Single Cell Proteomics v3 Open

Andrew Leduc · 2022

Protocol for preparing single cells for mass-spec analysis by nPOP as described by Leduc et al., 2021, 2022 DOI: 10.1186/s13059-022-02817-5. nPOP uses piezo acoustic dispensing to isolate individual cells in 300 picoliter volumes and perfo…

Highly Parallel Droplet Sample Preparation for Single Cell Proteomics v2 Open

Andrew Leduc, R. Gray Huffman, Joshua Cantlon, Saad Khan, Nikolai Slavov · 2022

Protocol for preparing single cells for mass-spec analysis by nPOP as described by Leduc et al., 2021, 2022 DOI: 10.1101/2021.04.24.441211. nPOP uses piezo acoustic dispensing to isolate individual cells in 300 picoliter volumes and perfor…

Highly Parallel Droplet Sample Preparation for Single Cell Proteomics v2 Open

Andrew Leduc, R. Gray Huffman, Saad Khan, Nikolai Slavov · 2022

Protocol for preparing single cells for mass-spec analysis by nPOP as described by Leduc et al., 2021, 2022 DOI: 10.1101/2021.04.24.441211. nPOP uses piezo acoustic dispensing to isolate individual cells in 300 picoliter volumes and perfor…

Prioritized single-cell proteomics reveals molecular and functional polarization across primary macrophages Open

R. Gray Huffman, Andrew Leduc, Christoph Wichmann, Marco Di Gioia, Francesco Borriello , et al. · 2022

Major aims of single-cell proteomics include increasing the consistency, sensitivity, and depth of protein quantification, especially for proteins and modifications of biological interest. To simultaneously advance all these aims, we devel…

Increasing the throughput of sensitive proteomics by plexDIA Open

Jason Derks, Andrew Leduc, Georg Wallmann, R. Gray Huffman, Matthew Willetts , et al. · 2021

Current mass-spectrometry methods enable high-throughput proteomics of large sample amounts, but proteomics of low sample amounts remains limited in depth and throughput. To increase the throughput of sensitive proteomics, we developed an …

Multiplexed single-cell proteomics using SCoPE2 Open

Aleksandra A. Petelski, Emily H Emmott, Andrew Leduc, R. Gray Huffman, Harrison Specht , et al. · 2021

Exploring functional protein covariation across single cells using nPOP Open

Andrew Leduc, R. Gray Huffman, Joshua Cantlon, Saad Khan, Nikolai Slavov · 2021

Many biological processes, such as the cell division cycle, are reflected in protein covariation across single cells. This covariation can be quantified and interpreted by single-cell mass-spectrometry (MS) with sufficiently high throughpu…

Multiplexed single-cell proteomics using SCoPE2 Open

Aleksandra A. Petelski, Edward Emmott, Andrew Leduc, R. Gray Huffman, Harrison Specht , et al. · 2021

Many biological systems are composed of diverse single cells. This diversity necessitates functional and molecular single-cell analysis. Single-cell protein analysis has long relied on affinity reagents, but emerging mass-spectrometry meth…

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