Nikolai Slavov

Nikolai Slavov
Northeastern University | NEU · Bioengineering Department

PhD

About

102
Publications
52,382
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
6,050
Citations
Introduction
My laboratory aims to understand the rules governing emergent systems-level behavior and to use them to rationally engineer biological systems. We make quantitative measurements, often at the single-cell level, to test different conceptual frameworks and discriminate among different classes of models. Areas of focus include: • Ribosome mediated translational regulation: Mechanisms by which ribosomal modifications regulate protein synthesis • Single-cell protein analysis: http://slavovlab.net
Additional affiliations
September 2015 - present
Northeastern University
Position
  • Professor (Assistant)
Description
  • I seek principles in the coordination among protein synthesis, metabolism, cell growth and differentiation. http://www.northeastern.edu/slavovlab/
January 2015 - present
Broad Institute of MIT and Harvard
Position
  • Affiliation
Description
  • Many protein isoforms - arising from alternative splicing, post-translational modifications (PTMs), or paralogous genes - have distinct biological functions. I develop methods allowing unprecedented accuracy (error < 10%) in quantifying protein isoforms.
January 2014 - August 2015
Harvard University
Position
  • Fellow
Description
  • I obtained direct evidence for differential stoichiometry among core ribosomal proteins in unperturbed wild-type cells, supporting the existence of ribosomes with distinct protein composition and physiological function.
Education
September 2004 - May 2010
Princeton University
Field of study
  • Molecular Biology
September 2001 - May 2004

Publications

Publications (102)
Article
Full-text available
Fermentating glucose in the presence of enough oxygen to support respiration, known as aerobic glycolysis, is believed to maximize growth rate. We observed increasing aerobic glycolysis during exponential growth, suggesting additional physiological roles for aerobic glycolysis. We investigated such roles in yeast batch cultures by quantifying O2 co...
Article
Full-text available
Understanding the regulation and structure of ribosomes is essential to understanding protein synthesis and its deregulation in disease. While ribosomes are believed to have a fixed stoichiometry among their core ribosomal proteins (RPs), some experiments suggest a more variable composition. Testing such variability requires direct and precise quan...
Article
Full-text available
Some exciting biological questions require quantifying thousands of proteins in single cells. To achieve this goal, we develop Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS) and validate its ability to identify distinct human cancer cell types based on their proteomes. We use SCoPE-MS to quantify over a thousand proteins in differentiating...
Article
Full-text available
Recently, the throughput of single-cell RNA-sequencing (transcriptomics) and genomics technologies has increased more than a 1000-fold. This increase has powered new analyses: Whereas traditional analysis of bulk tissue averages all differences between the diverse cells comprising such samples, single-cell analysis characterizes each individual cel...
Article
Full-text available
Background Macrophages are innate immune cells with diverse functional and molecular phenotypes. This diversity is largely unexplored at the level of single-cell proteomes because of the limitations of quantitative single-cell protein analysis. Results To overcome this limitation, we develop SCoPE2, which substantially increases quantitative accur...
Article
All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 year projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to tran...
Preprint
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 performs all subsequent preparation steps in small droplets on a fluorocarbon-coated slide. This design enables simul...
Preprint
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 performs all subsequent preparation steps in small droplets on a fluorocarbon-coated slide. This design enables simul...
Preprint
Full-text available
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 of these aims, we developed prioritized Single Cell ProtEomics (pSCoPE). pSCoPE ensures duty-cycle time for analyzing prioritized p...
Article
Full-text available
Technologies for counting protein molecules are enabling single-cell proteomics at increasing depth and scale. New advances in single-molecule methods by Brinkerhoff and colleagues promise to further increase the sensitivity of protein analysis and motivate questions about scaling up the counting of the human proteome.
Article
Full-text available
Biological functions arise from protein interactions, which are reflected in the natural variation of proteome configurations across individual cells. Emerging single-cell proteomics methods may decode this variation and empower inference of biological mechanisms with minimal assumptions.
Preprint
Current mass-spectrometry methods enable high-throughput proteomics of large sample amounts, but proteomics of low sample amounts remains limited in depth and throughput. We aimed to increase the throughput of high-sensitivity proteomics while achieving high proteome coverage and quantitative accuracy. We developed a general experimental and comput...
Article
Full-text available
Macrophages undergoing M1- versus M2-type polarization differ significantly in their cell metabolism and cellular functions. Here, global quantitative time-course proteomics and phosphoproteomics paired with transcriptomics provide a comprehensive characterization of temporal changes in cell metabolism, cellular functions, and signaling pathways th...
Article
Full-text available
Single-cell tandem mass-spectrometry (MS) has enabled analyzing hundreds of single cells per day and quantifying thousands of proteins across the cells. The broad dissemination of these capabilities can empower the dissection of pathophysiological mechanisms in heterogeneous tissues. Key requirements for achieving this goal include robust protocols...
Article
Full-text available
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 methods (either label-free or multiplexed) have enabled quantifying >1,000 proteins per cell while simultaneously i...
Preprint
Many biological functions, such as the cell division cycle, are intrinsically single-cell processes regulated in part by protein synthesis and degradation. Investigating such processes has motivated the development of single-cell mass spectrometry (MS) proteomics. To further advance single-cell MS proteomics, we developed a method for high throughp...
Preprint
Full-text available
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 methods (either label-free or multiplexed) have enabled quantifying over 1,000 proteins per cell while simultaneous...
Article
Full-text available
What will be the most important areas of research in biotech over the coming years? Which technologies will be most important to advance knowledge and applications in these areas? Nature Biotechnology reached out to a set of faculty doing outstanding work in research areas representative of the journal’s remit and asked them to contribute their vis...
Article
A new dimension for analyzing mass spectrometry data allows rapid quantification of up to 70% more peptides.
Article
Full-text available
Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made such analysis feasible for nucleic acids but single-cell protein analysis remains limited. Mass spectrometry is...
Article
Full-text available
The isobaric carrier approach, which combines small isobarically labeled samples with a larger isobarically labeled carrier sample, finds diverse applications in ultrasensitive mass spectrometry analysis of very small samples, such as single cells. To enhance the growing use of isobaric carriers, we characterized the trade-offs of using isobaric ca...
Preprint
Full-text available
The isobaric carrier approach, which combines small isobarically-labeled samples with a larger isobarically-labeled carrier sample, is finding diverse applications in ultrasensitive mass-spectrometry analysis of very small samples, such as single cells. To enhance the growing use of isobaric carriers, we characterized the trade-offs of using isobar...
Article
Full-text available
Increasing evidence suggests that ribosomes actively regulate protein synthesis. However, much of this evidence is indirect, leaving this layer of gene regulation largely unexplored, in part due to methodological limitations. Indeed, we review evidence demonstrating that commonly used methods, such as transcriptomics, are inadequate because the var...
Article
Full-text available
The fate and physiology of individual cells are controlled by protein interactions. We recently developed SCoPE-MS, a method for direct analysis of proteomes of single cells by LC-MS/MS. SCoPE-MS is enabled by isobaric-tag multiplexing of peptides from single cells together with carrier material, which serves both to minimize sample losses to equip...
Preprint
Full-text available
Increasing evidence suggests that ribosomes actively regulate protein synthesis. However, much of this evidence is indirect, leaving this layer of gene regulation largely unexplored, in part due to methodological limitations. Indeed, we review evidence demonstrating that commonly used methods, such as transcriptomics, are inadequate because the var...
Preprint
Full-text available
Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made such analysis feasible for nucleic acids, but single-cell protein analysis remains limited. Mass-spectrometry i...
Article
To mark the 15th anniversary of Nature Methods, we asked scientists from across diverse fields of basic biology research for their views on the most exciting and essential methodological challenges that their communities are poised to tackle in the near future.
Article
Full-text available
Analysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. This process, however, remains challenging for smaller samples, such as the proteomes of single mammalian cells, because reduced protein levels reduce th...
Preprint
Full-text available
The fate and physiology of individual cells are controlled by networks of proteins. Yet, our ability to quantitatively analyze protein networks in single cells has remained limited. To overcome this barrier, we developed SCoPE2. It integrates concepts from Single-Cell ProtEomics by Mass Spectrometry (SCoPE-MS) with automated and miniaturized sample...
Article
The performance of ultrasensitive LC-MS/MS methods, such as Single-Cell Proteomics by Mass Spectrometry (SCoPE-MS), depends on multiple interdependent parameters. This interdependence makes it challenging to specifically pinpoint sources of problems in the LC-MS/MS methods and approaches for resolving them. For example, low signal at MS2 level can...
Article
• Download : Download high-res image (523KB) • Download : Download full-size image Contrary to the textbook model, recent measurements demonstrated unexpected diversity in ribosomal composition that likely enables specialized translational functions. Methods based on liquid chromatography coupled to tandem mass-spectrometry (LC-MS/MS) enable direc...
Preprint
Full-text available
The performance of ultrasensitive LC-MS/MS methods, such as Single-Cell Proteomics by Mass Spectrometry (SCoPE-MS), depends on multiple interdependent parameters. This interdependence makes it challenging to specifically pinpoint bottlenecks in the LC-MS/MS methods and approaches for resolving them. For example, low signal at MS2 level can be due t...
Article
Full-text available
The existence of eukaryotic ribosomes with distinct ribosomal protein (RP) stoichiometry and regulatory roles in protein synthesis has been speculated for over 60 years. Recent advances in mass spectrometry (MS) and high-throughput analysis have begun to identify and characterize distinct ribosome stoichiometry in yeast and mammalian systems. In ad...
Preprint
Full-text available
A major limitation to applying quantitative LC-MS/MS proteomics to small samples, such as single cells, are the losses incured during sample cleanup. To relieve this limitation, we developed a Minimal ProteOmic sample Preparation (mPOP) method for culture-grown mam-malian cells. mPOP obviates cleanup and thus eliminates cleanup-related losses while...
Preprint
Full-text available
Analysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. This process, however, remains challenging for smaller samples, such as the proteomes of single mammalian cells, because reduced protein levels reduce th...
Article
Full-text available
The cellular abundance of proteins can vary even between isogenic single cells. This variability between single-cell protein levels can have regulatory roles, such as controlling cell fate during apoptosis induction or the proliferation/quiescence decision. Here, we review examples connecting protein levels and their dynamics in single cells to cel...
Preprint
Full-text available
Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the limitations of existing methods for quantifying protein levels in single cells. To alleviate these limitations, we developed Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS), and v...
Article
Full-text available
Many pressing medical challenges - such as diagnosing disease, enhancing directed stem cell differentiation, and classifying cancers - have long been hindered by limitations in our ability to quantify proteins in single cells. Mass-spectrometry (MS) is poised to transcend these limitations by developing powerful methods to routinely quantify thousa...
Preprint
Full-text available
Many pressing medical challenges - such as diagnosing disease, enhancing directed stem cell differentiation, and classifying cancers - have long been hindered by limitations in our ability to quantify proteins in single cells. Mass-spectrometry (MS) is poised to transcend these limitations by developing powerful methods to routinely quantify thousa...
Preprint
Many pressing medical challenges - such as diagnosing disease, enhancing directed stem cell differentiation, and classifying cancers - have long been hindered by limitations in our ability to quantify proteins in single cells. Mass-spectrometry (MS) is poised to transcend these limitations by developing powerful methods to routinely quantify thousa...
Preprint
Full-text available
The existence of eukaryotic ribosomes with distinct ribosomal protein (RP) stoichiometry and regulatory roles in protein synthesis been speculated for over sixty years. Recent advances in mass spectrometry and high throughput analysis have begun to identify and characterize distinct ribosome stoichiometry in yeast or mammalian systems. In addition...
Preprint
Full-text available
The existence of eukaryotic ribosomes with distinct ribosomal protein (RP) stoichiometry and regulatory roles in protein synthesis been speculated for over sixty years. Recent advances in mass spectrometry and high throughput analysis have begun to identify and characterize distinct ribosome stoichiometry in yeast or mammalian systems. In addition...
Preprint
Full-text available
The cellular abundance of proteins can vary even between isogenic single cells. This variability between single-cell protein levels can have functional roles, such as controlling cell fate during apoptosis induction or the proliferation/quiescence decision. Here, we review such examples of connecting protein levels and their dynamics in single cell...
Preprint
Full-text available
The cellular abundance of proteins can vary even between isogenic single cells. This variability between single-cell protein levels can have functional roles, such as controlling cell fate during apoptosis induction or the proliferation/quiescence decision. Here, we review such examples of connecting protein levels and their dynamics in single cell...
Article
Full-text available
Many pressing medical challenges - such as diagnosing disease, enhancing directed stem cell differentiation, and classifying cancers - have long been hindered by limitations in our ability to quantify proteins in single cells. Mass-spectrometry (MS) is poised to transcend these limitations by developing powerful methods to routinely quantify thousa...
Preprint
Full-text available
Many pressing medical challenges -- such as diagnosing disease, enhancing directed stem cell differentiation, and classifying cancers -- have long been hindered by limitations in our ability to quantify proteins in single cells. Mass-spectrometry (MS) is poised to transcend these limitations by developing powerful methods to routinely quantify thou...
Article
Full-text available
Many proteoforms - arising from alternative splicing, post-translational modifications (PTMs), or paralogous genes - have distinct biological functions, such as histone PTM proteoforms. However, their quantification by existing bottom-up mass-spectrometry (MS) methods is undermined by peptide-specific biases. To avoid these biases, we developed and...
Preprint
Full-text available
Many proteoforms – arising from alternative splicing, post-translational modifications (PTMs), or paralogous genes – have distinct biological functions, such as histone PTM proteoforms. However, their quantification by existing bottom-up mass–spectrometry (MS) methods is undermined by peptide-specific biases. To avoid these biases, we developed and...
Preprint
During in vitro differentiation, pluripotent stem cells undergo extensive remodeling of their gene expression profile. While studied extensively at the transcriptome level, much less is known about protein dynamics. Here, we measured mRNA and protein levels of 7459 genes during differentiation of embryonic stem cells (ESCs). This comprehensive data...
Article
Full-text available
Transcriptional and post-transcriptional regulation shape tissue-type-specific proteomes, but their relative contributions remain contested. Estimates of the factors determining protein levels in human tissues do not distinguish between (i) the factors determining the variability between the abundances of different proteins, i.e., mean-level-variab...
Data
Estimates of relative protein-to-RNA (rPTR) ratio for GO terms reproduce across different datasets. Pearson correlations between two estimates of the median rPTR ratios for all GO terms indicate reproducible effects in all tissues. As in Fig 2, rPTR estimates are derived using independent data sources. The lower and upper estimates are the endpoint...
Data
The total protein variance explained by scaled mRNA levels is not indicative of the correlations between mRNA and protein fold-changes across the corresponding tissue pairs. (a-c, top row), protein versus mRNA in kidney, liver and prostate. (d-f, middle row) protein versus scaled mRNA in kidney, liver and prostate. The only difference from the top...
Data
Fraction of across-tissues variability in protein levels explained by RNA variability for different functional gene sets. (a) The distributions of across-tissues correlations for gene sets defined by the gene ontology are shown as boxplots. The reliability of RNA and protein are estimated as the correlations between estimates from different dataset...
Data
Reproducibility of rPTR ratios estimated from different datasets. The x-axes shows estimates from Wilhelm et al. [20] and the y-axes estimates from Kim et al. [21]. (PDF)
Data
Peptide levels across human tissues. A zip-archived comma-delimited text file with estimates of peptide levels across 13 human tissues: adrenal gland, colon, esophagus, kidney, liver, lung, ovary, pancreas, prostate, testis, spleen, stomach, and heart. This file contains all peptide levels (integrated precursors areas) estimated from the MaxQuant s...
Data
Estimates of relative protein-to-RNA (rPTR) ratio for genes reproduce across different datasets. Correlations between the two estimates of rPTR ratios for all genes indicate reproducible effects in all tissues. The rPTR ratios were estimated independently from different datasets (as in Fig 2). The lower and upper estimates are the endpoints of the...
Data
Consensus dataset of protein levels across human tissues. A zip-archived comma-delimited text file with consensus estimates of protein levels across 13 human tissues: adrenal gland, colon, esophagus, kidney, liver, lung, ovary, pancreas, prostate, testis, spleen, stomach, and heart. (ZIP)
Article
Full-text available
The innate immune response is a central element of the initial defense against bacterial and viral pathogens. Macrophages are key innate immune cells that upon encountering pathogen-associated molecular patterns respond by producing cytokines, including IFN-β. In this study, we identify a novel role for RIPK1 and RIPK3, a pair of homologous serine/...
Preprint
Full-text available
Transcriptional and post-transcriptional regulation shape tissue-type-specific proteomes, but their relative contributions remain contested. Estimates of the factors determining protein levels in human tissues do not distinguish between ( i ) the factors determining the variability between the abundances of different proteins, i.e., mean-level-vari...
Preprint
Full-text available
Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the limitations of existing methods for quantifying protein levels in single cells. To alleviate these limitations, we developed Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS), and v...
Preprint
Full-text available
Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the limitations of existing methods for quantifying protein levels in single cells. To alleviate these limitations, we developed Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS), and v...
Article
Full-text available
Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the limitations of existing methods for quantifying protein levels in single cells. To alleviate these limitations, we developed Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS), and v...
Article
Full-text available
Two dimensional Difference Gel Electrophoresis (2-D DIGE) and mass spectrometry were applied to investigate the changes in metabolic proteins that occur over a seven day (day 1, 3 and 7) post mortem ageing period in porcine centrifugal exudate from divergent meat quality phenotypes. The objectives of the research were to enhance our understanding o...
Data
Biological function of the identified protein/fragment spots in porcine centrifugal drip (phenotypes and time course comparisons). aSpot numbers refer to Fig 3 in [15]. bBiological process of the proteins obtained using PANTHER analysis [25]. cComparison where the protein was significantly different [phenotype (PH), time course (TC)]. (DOC)
Data
Identified protein/fragment spots in porcine centrifugal drip with Peaks Studio 6. aSpot numbers refers to Fig 3 in our previous study [15]. bMolecular weight of the protein. (DOC)
Data
Representative 2-D DIGE gel images which show the 22 new spots identified by PEAKS Studio 6. Centrifugal drip proteins were separated by 2-D DIGE using immobilised pH 4–7 gradients (24 cm, linear) in the first dimension and 12% SDS-PAGE in the second dimension. The gel image is from a CyDye3-labelled reference sample (pool of all samples used). Thi...
Article
Full-text available
In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring au...
Article
Full-text available
About a decade ago, I observed that as the cell growth rate increases, mRNAs coding for ribosomal proteins are transcriptionally induced to varying degrees. This observation puzzled me as it defied my expectation that faster growing cells meet their demands for increased protein synthesis by simply inducing all ribosomal proteins to the same degree...
Article
Full-text available
About a decade ago, I observed that as the cell growth rate increases, mRNAs coding for ribosomal proteins are transcriptionally induced to varying degrees. This observation puzzled me as it defied my expectation that faster growing cells meet their demands for increased protein synthesis by simply inducing all ribosomal proteins to the same degree...