Chemical Decrosslinking-Based Peptide Characterization of Formaldehyde-Fixed Rat Pancreas Using Fluorescence-Guided Single-Cell Mass Spectrometry

Article Chemistry, Analytical

Label-Free Profiling of up to 200 Single-Cell Proteomes per DayUsing a Dual-Column Nanoflow Liquid Chromatography Platform

Kei G. I. Webber et al.

Summary: Single-cell proteomics has the potential to advance biomedical research and personalized medicine. A two-column liquid chromatography system is developed to improve the throughput and efficiency of label-free single-cell proteomics.

ANALYTICAL CHEMISTRY (2022)

Add to Collection

Article Chemistry, Analytical

Controllable Fabrication of Small-Size Holding Pipets for the Nondestructive Manipulation of Suspended Living Single Cells

Yuanyuan Wu et al.

Summary: This study proposed a method for the controllable fabrication of small-size holding pipets and achieved the active capture, movement, and sampling of suspended single cells. Moreover, the extracted compounds were successfully detected using an electrochemical method.

ANALYTICAL CHEMISTRY (2022)

Add to Collection

Article Chemistry, Analytical

'On the Spot' Digital Pathology of Breast Cancer Based on Single-Cell Mass Spectrometry Imaging

Eva Cuypers et al.

Summary: This study explores the molecular pathology of breast cancer using mass spectrometry imaging (MSI). By analyzing and visualizing at the single-cell level, it enables accurate and rapid diagnosis and prognosis within tissue sections. A molecular library was built, and a recognition model for breast cancer subtype, hormone status, and genotype based on metabolic phenotypes was established using deep learning. Our recognition models were also applied to complex tissue samples, identifying cell subtypes within seconds during measurement.

ANALYTICAL CHEMISTRY (2022)

Add to Collection

Article Chemistry, Multidisciplinary

Quantification of Biocatalytic Transformations by Single Microbial Cells Enabled by Tailored Integration of Droplet Microfluidics and Mass Spectrometry

Konstantin Wink et al.

Summary: Chemically specific and quantifiable monitoring of biocatalytic transformations at the single-cell level has been achieved through the integration of droplet microfluidics, cell imaging, and mass spectrometry.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2022)

Add to Collection

Article Chemistry, Multidisciplinary

Capillary Electrophoresis Mass Spectrometry for Scalable Single-Cell Proteomics

Bowen Shen et al.

Summary: This study demonstrates the scalability of capillary microsampling CE-ESI-HRMS for single-cell proteomics across broad cellular dimensions. The technique showed high sensitivity and speed compared to nanoLC, another commonly used single-cell technology. It can identify different proteins in cells and is suitable for subcellular proteomics.

FRONTIERS IN CHEMISTRY (2022)

Add to Collection

Article Chemistry, Analytical

Label-Free and Noninvasive Single-Cell Characterization for the Viscoelastic Properties of Cryopreserved Human Red Blood Cells Using a Dielectrophoresis-On-a-Chip Approach

Qianqian Hu et al.

Summary: In this study, we investigated the effects of cryopreservation on the biomechanics of human red blood cells using a microfluidic electrodeformation assay. Our findings showed that the viscoelasticity of the red blood cell membrane differed between permeable and impermeable cryoprotectants. Furthermore, we found that high freeze-thaw recovery did not necessarily indicate excellent viscoelasticity in the recovered cells. Our results highlight the importance of assessing single-cell viscoelasticity as an indicator for evaluating the quality of cryopreserved cells and improving our understanding of the cryoinjury mechanism. This assessment technique also holds significant potential for optimizing cryopreservation processes and screening optimal cryoprotectants.

ANALYTICAL CHEMISTRY (2022)

Add to Collection

Article Biochemistry & Molecular Biology

Profiling 26,000 Aplysia californica neurons by single cell mass spectrometry reveals neuronal populations with distinct neuropeptide profiles

Peter C. Chan-Andersen et al.

Summary: This study used microscopy-guided, high-throughput mass spectrometry to investigate the neuropeptide heterogeneity in the California sea hare. They identified 40 unique neuronal populations with distinct neuropeptide profiles, some of which were behaviorally related. This mass spectrometry-based approach offers a robust categorization of large cell populations based on single cell neuropeptide content and can be applied to various animals and tissues.

JOURNAL OF BIOLOGICAL CHEMISTRY (2022)

Add to Collection

Article Biochemical Research Methods

In-Depth Mass Spectrometry-Based Proteomics of Formalin-Fixed, Paraffin-Embedded Tissues with a Spatial Resolution of 50-200 μm

Andikan J. Nwosu et al.

Summary: This study modified a sample processing workflow to extract proteins from FFPE tissues and analyze protein expression. By optimizing the extraction conditions, a high-confidence proteome was obtained, and the protein coverage for FFPE tissues reached 88% compared to frozen tissues.

JOURNAL OF PROTEOME RESEARCH (2022)

Add to Collection

Article Biochemical Research Methods

Spatial Multiomics of Lipids, N-Glycans, and Tryptic Peptides on a Single FFPE Tissue Section

Vanna Denti et al.

Summary: Mass spectrometry imaging (MSI) is an emerging technology that allows mapping of molecular distribution in pathological tissues. This study presents a novel workflow for sequential MSI of lipids, N-glycans, and tryptic peptides on FFPE tissues, highlighting its enhanced molecular characterization.

JOURNAL OF PROTEOME RESEARCH (2022)

Add to Collection

Article Chemistry, Analytical

Single-Cell Metabolomics by Mass Spectrometry: Opportunities and Challenges

Marjan Dolatmoradi et al.

Summary: Cellular heterogeneity is an important property of cell populations that can be studied through single-cell metabolomics, which reveals molecular information and variations in metabolite concentrations. Mass spectrometry techniques face challenges in analyzing single cells, but can potentially uncover cellular synergism through tissue-embedded cell analysis.

ANALYSIS & SENSING (2022)

Add to Collection

Article Biochemical Research Methods

Image-guided MALDI mass spectrometry for high-throughput single-organelle characterization

Daniel C. Castro et al.

Summary: This article presents a workflow for image-guided MALDI MS characterization of peptide and lipid content in single organelles, allowing observation of the chemical heterogeneity within and between dense-core vesicles and lucent vesicles.

NATURE METHODS (2021)

Add to Collection

Article Biochemical Research Methods

Multiplexed single-cell proteomics using SCoPE2

Aleksandra A. Petelski et al.

Summary: The study introduces the SCoPE2 protocol for single-cell protein analysis, which utilizes isobaric mass tags for labeling and achieves cost-effective quantitative protein analysis.

NATURE PROTOCOLS (2021)

Add to Collection

Article Multidisciplinary Sciences

High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip

Jongmin Woo et al.

Summary: This study introduces a nested nanoPOTS (N2) chip to improve protein recovery, operation robustness, and processing throughput for isobaric-labeling-based single-cell proteomics workflow. The N2 chip enables robust quantification of approximately 1500 proteins and reveals membrane protein markers, demonstrating high stability of single-cell proteome profiles for cells cultured under identical conditions.

NATURE COMMUNICATIONS (2021)

Add to Collection

Article Chemistry, Analytical

Successive High-Resolution (H2O)n-GC1B and C60-SIMS Imaging Integrates Multi-Omics in Different Cell Types in Breast Cancer Tissue

Hua Tian et al.

Summary: This study developed a new methodology for comprehensive lipidomic and metabolomic profiling of individual cells on frozen-hydrated tissue sections, combined with cell-type specific lanthanide antibodies analysis. The research revealed distinct variations of distribution and intensities of key ions in different types of cells within the tumor microenvironment. The feasibility of employing SIMS imaging for multi-omics profiling at the single-cell level in the same tissue section opens up possibilities for gaining new insights into cellular interactions in various tissue microenvironments.

ANALYTICAL CHEMISTRY (2021)

Add to Collection

Article Biochemical Research Methods

Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing

Paul Datlinger et al.

Summary: The development of 'single-cell combinatorial fluidic indexing' (scifi) allows for cost-effective single-cell sequencing on a massive scale, combining preindexing of entire transcriptomes with single-cell RNA-seq using microfluidics. This approach significantly increases throughput and enables sample multiplexing in a straightforward manner.

NATURE METHODS (2021)

Add to Collection

Article Chemistry, Multidisciplinary

Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell

Yongzheng Cong et al.

Summary: The combination of nanodroplet sample preparation, ultra-low-flow nanoLC, high-field asymmetric ion mobility spectrometry (FAIMS), and the latest-generation Orbitrap Eclipse Tribrid mass spectrometer led to greatly improved single-cell proteome profiling. FAIMS effectively filtered out singly charged ions, allowing for more effective MS analysis of multiply charged peptides, resulting in a significantly higher number of protein groups identified from single HeLa cells compared to traditional methods. Differential analysis also showed similar proteome coverage for single microdissected motor neurons and interneurons from human spinal tissue, with the ability to differentiate between the two subpopulations based on label-free quantification.

CHEMICAL SCIENCE (2021)

Add to Collection

Article Biochemical Research Methods

Are formalin-fixed and paraffin-embedded tissues fit for proteomic analysis?

Malte Bayer et al.

JOURNAL OF MASS SPECTROMETRY (2020)

Add to Collection

Editorial Material Multidisciplinary Sciences

Unpicking the proteome in single cells

Nikolai Slavov

SCIENCE (2020)

Add to Collection

Review Oncology

Advancing Cancer Research and Medicine with Single-Cell Genomics

Bora Lim et al.

CANCER CELL (2020)

Add to Collection

Article Chemistry, Analytical

Spatial proteome profiling by immunohistochemistry-based laser capture microdissection and data-independent acquisition proteomics

Peiwu Huang et al.

ANALYTICA CHIMICA ACTA (2020)

Add to Collection

Article Chemistry, Multidisciplinary

Removing Formaldehyde-Induced Peptidyl Crosslinks Enables Mass Spectrometry Imaging of Peptide Hormone Distributions from Formalin-Fixed Paraffin-Embedded Tissues

Dong-Kyu Lee et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2020)

Add to Collection

Article Biochemical Research Methods

Multimodal Imaging Mass Spectrometry: Next Generation Molecular Mapping in Biology and Medicine

Elizabeth K. Neumann et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2020)

Add to Collection

Article Biochemical Research Methods

MS Imaging-Guided Microproteomics for Spatial Omics on a Single Instrument

Frederic Dewez et al.

PROTEOMICS (2020)

Add to Collection

Article Chemistry, Analytical

Microsampling Capillary Electrophoresis Mass Spectrometry Enables Single-Cell Proteomics in Complex Tissues: Developing Cell Clones in Live Xenopus laevis and Zebrafish Embryos

Camille Lombard-Banek et al.

ANALYTICAL CHEMISTRY (2019)

Add to Collection

Article Chemistry, Multidisciplinary

Lipid Heterogeneity between Astrocytes and Neurons Revealed by Single-Cell MALDI-MS Combined with Immunocytochemical Classification

Elizabeth K. Neumann et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2019)

Add to Collection

Article Chemistry, Analytical

Lipid Analysis of 30 000 Individual Rodent Cerebellar Cells Using High-Resolution Mass Spectrometry

Elizabeth K. Neumann et al.

ANALYTICAL CHEMISTRY (2019)

Add to Collection

Article Biochemical Research Methods

Best Practices for Preparing a Single Cell Suspension from Solid Tissues for Flow Cytometry

Andrew Reichard et al.

CYTOMETRY PART A (2019)

Add to Collection

Review Endocrinology & Metabolism

Extracellular Matrix-Associated Factors Play Critical Roles in Regulating Pancreatic β-Cell Proliferation and Survival

Shannon E. Townsend et al.

ENDOCRINOLOGY (2019)

Add to Collection

Review Medical Laboratory Technology

The importance of clinical tissue imaging

Jeffrey M. Spraggins et al.

CLINICAL MASS SPECTROMETRY (2019)

Add to Collection

Article Biochemical Research Methods

Mapping Extracellular Matrix Proteins in Formalin-Fixed, Paraffin-Embedded Tissues by MALDI Imaging Mass Spectrometry

Peggi M. Angel et al.

JOURNAL OF PROTEOME RESEARCH (2018)

Add to Collection

Review Chemistry, Multidisciplinary

Single-Cell Mass Spectrometry Approaches to Explore Cellular Heterogeneity

Linwen Zhang et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2018)

Add to Collection

Article Biotechnology & Applied Microbiology

SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation

Bogdan Budnik et al.

GENOME BIOLOGY (2018)

Add to Collection

Article Biochemical Research Methods

microMS: A Python Platform for Image-Guided Mass Spectrometry Profiling

Troy J. Comi et al.

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY (2017)

Add to Collection

Article Biochemistry & Molecular Biology

Single Cell Peptide Heterogeneity of Rat Islets of Langerhans

Erik T. Janson et al.

ACS CHEMICAL BIOLOGY (2016)

Add to Collection

Article Cell Biology

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes

Asa Segerstolpe et al.

CELL METABOLISM (2016)

Add to Collection

Article Chemistry, Analytical

Classification of Large Cellular Populations and Discovery of Rare Cells Using Single Cell Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

Ta-Hsuan Ong et al.

ANALYTICAL CHEMISTRY (2015)

Add to Collection

Review Biochemistry & Molecular Biology

Proteomic developments in the analysis of formalin-fixed tissue

Ove J. R. Gustafsson et al.

BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS (2015)

Add to Collection

Review Genetics & Heredity

Single-cell sequencing-based technologies will revolutionize whole-organism science

Ehud Shapiro et al.

NATURE REVIEWS GENETICS (2013)

Add to Collection

Article Biochemical Research Methods

Matrix-assisted laser desorption/ionization imaging protocol for in situ characterization of tryptic peptide identity and distribution in formalin-fixed tissue

Ove J. R. Gustafsson et al.

RAPID COMMUNICATIONS IN MASS SPECTROMETRY (2013)

Add to Collection

Article Biochemistry & Molecular Biology

Targeted Single-Cell Microchemical Analysis: MS-Based Peptidomics of Individual Paraformaldehyde-Fixed and Immunolabeled Neurons

Susanne Neupert et al.

CHEMISTRY & BIOLOGY (2012)

Add to Collection

Article Biophysics

Thermal Denaturation Studies of Collagen by Microthermal Analysis and Atomic Force Microscopy

Laurent Bozec et al.

BIOPHYSICAL JOURNAL (2011)

Add to Collection

Article Biochemical Research Methods

Proteomic analysis of formalin-fixed paraffin-embedded tissue by MALDI imaging mass spectrometry

Rita Casadonte et al.

NATURE PROTOCOLS (2011)

Add to Collection

Article Chemistry, Analytical

Spatial profiling with MALDI MS: Distribution of neuropeptides within single neurons

SS Rubakhin et al.

ANALYTICAL CHEMISTRY (2003)

Add to Collection

Chemical Decrosslinking-Based Peptide Characterization of Formaldehyde-Fixed Rat Pancreas Using Fluorescence-Guided Single-Cell Mass Spectrometry

Related references

Export Citation

Share Paper