A5066505595- Advanced Proteomics Techniques and Applications
- Single-cell and spatial transcriptomics
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- SARS-CoV-2 and COVID-19 Research
- Advanced Biosensing Techniques and Applications
- Immune responses and vaccinations
- Immune cells in cancer
- Mitochondrial Function and Pathology
- Advanced biosensing and bioanalysis techniques
- Fungal and yeast genetics research
- RNA and protein synthesis mechanisms
- vaccines and immunoinformatics approaches
- Cell Adhesion Molecules Research
- Protease and Inhibitor Mechanisms
- Genetic Neurodegenerative Diseases
- Bioinformatics and Genomic Networks
- Protein Kinase Regulation and GTPase Signaling
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- Animal Virus Infections Studies
- Vaccine Coverage and Hesitancy
- Cellular transport and secretion
- Pluripotent Stem Cells Research
- Immunodeficiency and Autoimmune Disorders
Northeastern University
2018-2024
Universidad del Noreste
2020-2023
Broad Institute
2017-2022
Massachusetts Institute of Technology
2021
Abstract 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 limitations quantitative protein analysis. Results To overcome this limitation, we develop SCoPE2, which substantially increases accuracy throughput while lowering cost hands-on time by introducing automated miniaturized sample preparation. These advances enable us to analyze emergence cellular...
Major aims of single-cell proteomics include increasing the consistency, sensitivity and depth protein quantification, especially for proteins modifications biological interest. Here, to simultaneously advance all these aims, we developed prioritized Single-Cell ProtEomics (pSCoPE). pSCoPE consistently analyzes thousands peptides across single cells (thus data completeness) while maximizing instrument time spent analyzing identifiable peptides, thus proteome depth. These strategies increased...
A major limitation to applying quantitative LC-MS/MS proteomics small samples, such as single cells, are the losses incured during sample cleanup. To relieve this limitation, we developed a Minimal ProteOmic Preparation (mPOP) method for culture-grown mammalian cells. mPOP obviates cleanup and thus eliminates cleanup-related while expediting preparation simplifying its automation. Bulk SILAC samples processed by or conventional urea-based methods indicated that results in complete cell lysis...
The performance of ultrasensitive liquid chromatography and tandem mass spectrometry (LC-MS/MS) methods, such as single-cell proteomics by (SCoPE-MS), depends on multiple interdependent parameters. This interdependence makes it challenging to specifically pinpoint the sources problems in LC-MS/MS methods approaches for resolving them. For example, a low signal at MS2 level can be due poor LC separation, ionization, apex targeting, ion transfer, or detection. We sought diagnose interactively...
The isobaric carrier approach, which combines small isobarically labeled samples with a larger sample, finds diverse applications in ultrasensitive mass spectrometry analysis of very samples, such as single cells. To enhance the growing use carriers, we characterized trade-offs using carriers controlled experiments complex human proteomes. data indicate that directly peptide sequence identification without simultaneously increasing number protein copies sampled from samples. results also...
Abstract Macrophages are innate immune cells with diverse functional and molecular phenotypes. This diversity is largely unexplored at the level of single-cell proteomes because limitations quantitative protein analysis. To overcome this limitation, we developed SCoPE2, which substantially increases accuracy throughput while lowering cost hands-on time by introducing automated miniaturized sample preparation. These advances enable us to analyze emergence cellular heterogeneity as homogeneous...
Major aims of single-cell proteomics include increasing the consistency, sensitivity, and depth protein quantification, especially for proteins modifications biological interest. To simultaneously advance all these aims, we developed prioritized Single Cell ProtEomics (pSCoPE). pSCoPE consistently analyzes thousands peptides across single cells (thus data completeness) while analyzing identifiable at full duty-cycle, thus proteome depth. These strategies increased completeness, coverage over...
The throughput of mass spectrometry (MS) proteomics can be increased substantially by multiplexing that enables parallelization data acquisition. Such in the domain (plexDIA) and time (timePlex) increases density spectra overlap between ions originating from different precursors, potentially inhibiting analysis. To enhance sequence identification quantification such spectra, we developed an open source software for Joint Modeling spectra: JMod. It uses intrinsic structure explicitly models...
Mass spectrometry-based proteomics enables comprehensive characterization of protein abundance, function, and interactions. Label-free approaches are simple to implement but challenging scale thousands samples per day. Multiplexed techniques, such as plexDIA, can address these limitations remain restricted by the lack mass tags optimized for data-independent acquisition (DIA) workflows. Here, we present a systematic approach screening library 576 compounds that identifies several small...
Liquid chromatography-mass spectrometry (LC-MS) can enable precise and accurate quantification of analytes at high-sensitivity, but the rate which samples be analyzed remains limiting. Throughput increased by multiplexing in mass domain with plexDIA, yet along one dimension will only linearly scale throughput plex. To combinatorial-scaling proteomics we developed a complementary strategy time domain, termed `timePlex'. timePlex staggers overlaps separation periods individual samples. This is...
Current mass-spectrometry methods enable high-throughput proteomics of large sample amounts, but low amounts remains limited in depth and throughput. To increase the throughput sensitive proteomics, we developed an experimental computational framework, plexDIA, for simultaneously multiplexing analysis both peptides samples. Multiplexed with plexDIA increases multiplicatively number labels without reducing proteome coverage or quantitative accuracy. By using 3-plex nonisobaric mass tags,...
Loss-of-function mutations in the secreted enzyme ADAMTS7 (a disintegrin and metalloproteinase with thrombospondin motifs 7) are associated protection for coronary artery disease. catalytic inhibition has been proposed as a therapeutic strategy treating disease; however, lack of an endogenous substrate hindered development activity-based biomarkers. To identify extracellular substrates their cleavage sites relevant to vascular disease, we used TAILS (terminal amine isotopic labeling...
Bacillus Calmette-Guérin (BCG) protects against childhood tuberculosis; and unlike most vaccines, BCG broadly impacts immunity to other pathogens even some cancers. Early in the COVID-19 pandemic, epidemiological studies identified a protective association between vaccination outcomes of SARS-CoV-2, but associations later were inconsistent. We sought possible reasons noticed study populations often lived same country. Since individuals from regions can share common ancestors, we hypothesized...
Abstract Pre-patterning of the embryo, driven by spatially localized factors, is a common feature across several non-mammalian species 1–4 . However, mammals display regulative development and thus it was thought that blastomeres embryo do not show such pre-patterning, contributing randomly to three lineages blastocyst: epiblast, primitive endoderm trophectoderm will generate new organism, yolk sac placenta respectively 4–6 Unexpectedly, early mouse human embryos have been reported distinct...
Single-cell proteomics analysis requires sensitive, quantitatively accurate, widely accessible, and robust methods. To meet these requirements, the Single-Cell ProtEomics (SCoPE2) protocol was developed as a second-generation method for quantifying hundreds to thousands of proteins from limited samples, down level single cell. Experiments using this have achieved over 3,000 across 1,500 mammalian cells (500-1,000 per cell) in 10 days mass spectrometer instrument time. SCoPE2 leverages...
Abstract 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 simultaneously increasing the specificity quantification. Isobaric carrier based multiplexed proteomics is a scalable, reliable, cost-effective...
The isobaric carrier approach, which combines small isobarically-labeled samples with a larger sample, is finding diverse applications in ultrasensitive mass-spectrometry analysis of very samples, such as single cells. To enhance the growing use carriers, we characterized trade-offs using carriers controlled experiments complex human proteomes. data indicate that directly enhances peptide sequence identification without simultaneously increasing number protein copies sampled from samples....
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 single cells. Mass-spectrometry (MS) is poised transcend these developing powerful methods routinely thousands of proteoforms across many We outline specific technological developments ideas that can increase the sensitivity throughput MS orders magnitude usher this new age. These...