New Views of Old Proteins: Clarifying the Enigmatic Proteome

[1]  Lloyd M. Smith,et al.  Putting Humpty Dumpty Back Together Again: What Does Protein Quantification Mean in Bottom-Up Proteomics? , 2022, Journal of proteome research.

[2]  Edward L. Huttlin,et al.  A multi-scale map of cell structure fusing protein images and interactions , 2021, Nature.

[3]  N. Kelleher,et al.  The Human Proteoform Project: Defining the human proteome , 2021, Science advances.

[4]  B. Kuster,et al.  The emerging landscape of single-molecule protein sequencing technologies , 2021, Nature Methods.

[5]  A. deMello,et al.  High-throughput multiparametric imaging flow cytometry: toward diffraction-limited sub-cellular detection and monitoring of sub-cellular processes. , 2021, Cell reports.

[6]  Michael T. Eadon,et al.  Rationale and design of the Kidney Precision Medicine Project. , 2021, Kidney international.

[7]  S. Ricard-Blum,et al.  A guide to the composition and functions of the extracellular matrix , 2021, The FEBS journal.

[8]  A. Nairn,et al.  Exosomes as Emerging Biomarker Tools in Neurodegenerative and Neuropsychiatric Disorders—A Proteomics Perspective , 2021, Brain sciences.

[9]  M. Mann,et al.  AI-driven Deep Visual Proteomics defines cell identity and heterogeneity , 2021, bioRxiv.

[10]  Lloyd M. Smith,et al.  Can we put Humpty Dumpty back together again? What does protein quantification mean in bottom-up proteomics? , 2021, bioRxiv.

[11]  David H Perlman,et al.  Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2 , 2021, Genome biology.

[12]  Jay W. Shin,et al.  Building a high-quality Human Cell Atlas , 2021, Nature Biotechnology.

[13]  Lin He,et al.  Multimodal detection of protein isoforms and nucleic acids from mouse pre-implantation embryos , 2021, Nature Protocols.

[14]  Fabian J Theis,et al.  Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation , 2020, bioRxiv.

[15]  Meagan C. Burnet,et al.  High-Throughput Large-Scale Targeted Proteomics Assays for Quantifying Pathway Proteins in Pseudomonas putida KT2440 , 2020, Frontiers in Bioengineering and Biotechnology.

[16]  R. Drake,et al.  Multiplexed imaging mass spectrometry of the extracellular matrix using serial enzyme digests from formalin-fixed paraffin-embedded tissue sections , 2020, Analytical and Bioanalytical Chemistry.

[17]  Lloyd M. Smith,et al.  The Human Proteoform Project: A Plan to Define the Human Proteome , 2020 .

[18]  Rebekah L. Gundry,et al.  A high-stringency blueprint of the human proteome , 2020, Nature Communications.

[19]  Florian Schueder,et al.  DNA‐Barcoded Fluorescence Microscopy for Spatial Omics , 2020, Proteomics.

[20]  Yifan Cheng,et al.  Targeting phosphotyrosine in native proteins with conditional, bi-specific antibody traps. , 2020, Journal of the American Chemical Society.

[21]  Monya Baker,et al.  When antibodies mislead: the quest for validation , 2020, Nature.

[22]  Ryan T Kelly,et al.  Single-cell Proteomics: Progress and Prospects , 2020, Molecular & Cellular Proteomics.

[23]  Tao Liu,et al.  Proteomic Analysis of Exosomes for Discovery of Protein Biomarkers for Prostate and Bladder Cancer , 2020, Cancers.

[24]  Jens Hansen,et al.  Towards Building a Smart Kidney Atlas: Network-based integration of multimodal transcriptomic, proteomic, metabolomic and imaging data in the Kidney Precision Medicine Project , 2020 .

[25]  Ying Zhu,et al.  Automated Coupling of Nanodroplet Sample Preparation with Liquid Chromatography-Mass Spectrometry for High-Throughput Single-Cell Proteomics. , 2020, Analytical chemistry.

[26]  D. Weitz,et al.  Single Molecule Protein Detection with Attomolar Sensitivity Using Droplet Digital Enzyme-Linked Immunosorbent Assay. , 2020, ACS nano.

[27]  Jianzhu Ma,et al.  Mapping cell structure across scales by fusing protein images and interactions , 2020, bioRxiv.

[28]  Ying Zhu,et al.  Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell , 2020, bioRxiv.

[29]  Thomas H. Barker,et al.  Spatial-omics: Novel Approaches to Probe Cell Heterogeneity and Extracellular Matrix Biology. , 2020, Matrix biology : journal of the International Society for Matrix Biology.

[30]  Deyong Chen,et al.  Advances of Single-Cell Protein Analysis , 2020, Cells.

[31]  R. Caprioli,et al.  Discovering new lipidomic features using cell type specific fluorophore expression to provide spatial and biological specificity in a multimodal workflow with MALDI Imaging Mass Spectrometry. , 2020, Analytical chemistry.

[32]  Nikolai Slavov,et al.  Single-cell protein analysis by mass spectrometry. , 2020, Current opinion in chemical biology.

[33]  Nancy R. Zhang,et al.  The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution , 2020, Cell.

[34]  Lin He,et al.  Assessing heterogeneity among single embryos and single blastomeres using open microfluidic design , 2020, Science Advances.

[35]  Ying Zhu,et al.  An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics , 2020, Molecular & Cellular Proteomics.

[36]  Ying Zhu,et al.  Improved Single Cell Proteome Coverage Using Narrow-Bore Packed NanoLC Columns and Ultrasensitive Mass Spectrometry. , 2020, Analytical chemistry.

[37]  Ryan T. Kelly,et al.  Automated mass spectrometry imaging of over 2000 proteins from tissue sections at 100-μm spatial resolution , 2020, Nature Communications.

[38]  Heeva Baharlou,et al.  Mass Cytometry Imaging for the Study of Human Diseases—Applications and Data Analysis Strategies , 2019, Front. Immunol..

[39]  Ying Zhu,et al.  Single-cell proteomics reveals changes in expression during hair-cell development , 2019, eLife.

[40]  K. Clauser,et al.  MatrisomeDB: the ECM-protein knowledge database , 2019, Nucleic Acids Res..

[41]  A. Naba,et al.  Exploring the extracellular matrix in health and disease using proteomics. , 2019, Essays in biochemistry.

[42]  Ying Zhu,et al.  High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labelling in a Nanodroplet Sample Preparation Platform. , 2019, Analytical chemistry.

[43]  Joshua A. Klein,et al.  Proteomics, Glycomics, and Glycoproteomics of Matrisome Molecules* , 2019, Molecular & Cellular Proteomics.

[44]  Kristin E. Burnum-Johnson,et al.  High spatial resolution imaging of biological tissues using nanospray desorption electrospray ionization mass spectrometry , 2019, Nature Protocols.

[45]  B. Porse,et al.  Quantitative single-cell proteomics as a tool to characterize cellular hierarchies , 2019, Nature Communications.

[46]  Kai-Ping Chang,et al.  Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma* , 2019, Molecular & Cellular Proteomics.

[47]  Reinhard Dechant,et al.  Ultra High-Throughput Multiparametric Imaging Flow Cytometry: Towards Diffraction-Limited Sub-Cellular Detection , 2019, bioRxiv.

[48]  Kenneth M. Yamada,et al.  Extracellular matrix dynamics in cell migration, invasion and tissue morphogenesis , 2019, International journal of experimental pathology.

[49]  Hyungwon Choi,et al.  Exploiting Interdata Relationships in Next-generation Proteomics Analysis* , 2019, Molecular & Cellular Proteomics.

[50]  W. J. Perry,et al.  MicroLESA: Integrating Autofluorescence Microscopy, In Situ Micro-Digestions, and Liquid Extraction Surface Analysis for High Spatial Resolution Targeted Proteomic Studies. , 2019, Analytical chemistry.

[51]  Shila Ghazanfar,et al.  The human body at cellular resolution: the NIH Human Biomolecular Atlas Program , 2019, Nature.

[52]  Peter Nemes,et al.  Microsampling Capillary Electrophoresis Mass Spectrometry Enables Single-Cell Proteomics in Complex Tissues: Developing Cell Clones in Live Xenopus laevis and Zebrafish Embryos. , 2019, Analytical chemistry.

[53]  David Issadore,et al.  Mobile platform for rapid sub–picogram-per-milliliter, multiplexed, digital droplet detection of proteins , 2019, Proceedings of the National Academy of Sciences.

[54]  O. Eickelberg,et al.  Quantitative proteomic profiling of extracellular matrix and site-specific collagen post-translational modifications in an in vitro model of lung fibrosis , 2019, Matrix biology plus.

[55]  J. Yates,et al.  Understanding molecular mechanisms of disease through spatial proteomics. , 2019, Current opinion in chemical biology.

[56]  Jeffrey M Spraggins,et al.  Protein identification strategies in MALDI imaging mass spectrometry: a brief review. , 2019, Current opinion in chemical biology.

[57]  E. Lundberg,et al.  Spatial proteomics: a powerful discovery tool for cell biology , 2019, Nature Reviews Molecular Cell Biology.

[58]  Yana Safonova,et al.  De novo Inference of Diversity Genes and Analysis of Non-canonical V(DD)J Recombination in Immunoglobulins , 2019, Front. Immunol..

[59]  Cassandra L Clift,et al.  Extracellular Matrix Imaging of Breast Tissue Pathologies by MALDI–Imaging Mass Spectrometry , 2018, Proteomics. Clinical applications.

[60]  Jeffrey R. Whiteaker,et al.  Clinical potential of mass spectrometry-based proteogenomics , 2018, Nature Reviews Clinical Oncology.

[61]  Xiangmin Zhang,et al.  Integrated Proteome Analysis Device for Fast Single-Cell Protein Profiling. , 2018, Analytical chemistry.

[62]  Paul D Piehowski,et al.  Nanoproteomics comes of age , 2018, Expert review of proteomics.

[63]  Edward M Marcotte,et al.  Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures , 2018, Nature Biotechnology.

[64]  David W. Greening,et al.  Extracellular vesicles in cancer — implications for future improvements in cancer care , 2018, Nature Reviews Clinical Oncology.

[65]  C. Dekker,et al.  Paving the way to single-molecule protein sequencing , 2018, Nature Nanotechnology.

[66]  Alexander M. Franks,et al.  DART-ID increases single-cell proteome coverage , 2018, bioRxiv.

[67]  N. Slavov,et al.  Single cell protein analysis for systems biology. , 2018, Essays in biochemistry.

[68]  N. Slavov,et al.  SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation , 2017, Genome Biology.

[69]  N. Perrimon,et al.  Efficient proximity labeling in living cells and organisms with TurboID , 2018, Nature Biotechnology.

[70]  Ronald J. Moore,et al.  Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS. , 2018, Angewandte Chemie.

[71]  Min Huang,et al.  Nanoliter-Scale Oil-Air-Droplet Chip-Based Single Cell Proteomic Analysis. , 2018, Analytical chemistry.

[72]  Lloyd M. Smith,et al.  Proteoforms as the next proteomics currency , 2018, Science.

[73]  Ronald J. Moore,et al.  Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells , 2018, Nature Communications.

[74]  Lloyd M. Smith,et al.  How many human proteoforms are there? , 2018, Nature chemical biology.

[75]  Susana Comte-Walters,et al.  Mapping Extracellular Matrix Proteins in Formalin-Fixed, Paraffin-Embedded Tissues by MALDI Imaging Mass Spectrometry. , 2018, Journal of proteome research.

[76]  Justin T. Baca,et al.  Proteomic Characterization of Dermal Interstitial Fluid Extracted Using a Novel Microneedle-Assisted Technique. , 2018, Journal of proteome research.

[77]  Vanessa M. Peterson,et al.  Multiplexed quantification of proteins and transcripts in single cells , 2017, Nature Biotechnology.

[78]  H. Swerdlow,et al.  Large-scale simultaneous measurement of epitopes and transcriptomes in single cells , 2017, Nature Methods.

[79]  Devin P. Sullivan,et al.  A subcellular map of the human proteome , 2017, Science.

[80]  A. Herr,et al.  Subcellular western blotting of single cells , 2017, Microsystems & Nanoengineering.

[81]  M. Merchant,et al.  Characterization of glomerular extracellular matrix by proteomic analysis of laser-captured microdissected glomeruli. , 2017, Kidney international.

[82]  Emma Lundberg,et al.  A proposal for validation of antibodies , 2016, Nature Methods.

[83]  Amy E Herr,et al.  Single cell–resolution western blotting , 2016, Nature Protocols.

[84]  Eric P Skaar,et al.  Next‐generation technologies for spatial proteomics: Integrating ultra‐high speed MALDI‐TOF and high mass resolution MALDI FTICR imaging mass spectrometry for protein analysis , 2016, Proteomics.

[85]  Matthias Mann,et al.  Plasma Proteome Profiling to Assess Human Health and Disease. , 2016, Cell systems.

[86]  Gloria M. Sheynkman,et al.  Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing , 2016, Cell.

[87]  Lorenzo J. Vega-Montoto,et al.  Comprehensive Characterization of Glycosylation and Hydroxylation of Basement Membrane Collagen IV by High‐Resolution Mass Spectrometry , 2016, Journal of proteome research.

[88]  Li Ding,et al.  An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer* , 2015, Molecular & Cellular Proteomics.

[89]  Jeffrey R. Whiteaker,et al.  Immobilized Metal Affinity Chromatography Coupled to Multiple Reaction Monitoring Enables Reproducible Quantification of Phospho-signaling* , 2015, Molecular & Cellular Proteomics.

[90]  A. Herr,et al.  Microfluidics: reframing biological enquiry , 2015, Nature Reviews Molecular Cell Biology.

[91]  Alla Lapidus,et al.  IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis , 2015, Bioinform..

[92]  S. Carr,et al.  The extracellular matrix: Tools and insights for the "omics" era. , 2015, Matrix biology : journal of the International Society for Matrix Biology.

[93]  David N. Kennedy,et al.  The Resource Identification Initiative: A cultural shift in publishing , 2015, Neuroinformatics.

[94]  M. Baker Reproducibility crisis: Blame it on the antibodies , 2015, Nature.

[95]  Eric P Skaar,et al.  MALDI FTICR IMS of Intact Proteins: Using Mass Accuracy to Link Protein Images with Proteomics Data , 2015, Journal of The American Society for Mass Spectrometry.

[96]  Richard M. Caprioli,et al.  Fusion of mass spectrometry and microscopy: a multi-modality paradigm for molecular tissue mapping , 2015, Nature Methods.

[97]  Andreas Plückthun,et al.  Reproducibility: Standardize antibodies used in research , 2015, Nature.

[98]  Amy E. Herr,et al.  Single-cell western blotting , 2014, Nature Methods.

[99]  J. Stenvang,et al.  Homogenous 96-Plex PEA Immunoassay Exhibiting High Sensitivity, Specificity, and Excellent Scalability , 2014, PloS one.

[100]  R. Zubarev The challenge of the proteome dynamic range and its implications for in‐depth proteomics , 2013, Proteomics.

[101]  Lloyd M. Smith,et al.  Proteoform: a single term describing protein complexity , 2013, Nature Methods.

[102]  Neil L. Kelleher,et al.  A Cell-Based Approach to the Human Proteome Project , 2012, Journal of The American Society for Mass Spectrometry.

[103]  T. Ha,et al.  Single-molecule pull-down for studying protein interactions , 2012, Nature Protocols.

[104]  Steven A. Carr,et al.  The Matrisome: In Silico Definition and In Vivo Characterization by Proteomics of Normal and Tumor Extracellular Matrices , 2011, Molecular & Cellular Proteomics.

[105]  David M. Rissin,et al.  Single-Molecule enzyme-linked immunosorbent assay detects serum proteins at subfemtomolar concentrations , 2010, Nature Biotechnology.

[106]  Richard O. Hynes,et al.  The Extracellular Matrix: Not Just Pretty Fibrils , 2009, Science.

[107]  Takashi,et al.  RESOLUTION , 2009, Bring Now the Angels.

[108]  Luisa Montecchi-Palazzi,et al.  The PSI-MOD community standard for representation of protein modification data , 2008, Nature Biotechnology.

[109]  Alexey I Nesvizhskii,et al.  Interpretation of Shotgun Proteomic Data , 2005, Molecular & Cellular Proteomics.

[110]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[111]  U. Bhalla,et al.  Emergent properties of networks of biological signaling pathways. , 1999, Science.

[112]  John Marino,et al.  Strategies for Development of a Next-Generation Protein Sequencing Platform. , 2019, Trends in biochemical sciences.

[113]  J. Hörandel,et al.  COSMIC RAYS FROM THE KNEE TO THE SECOND , 2007 .

[114]  C. Johnson Progress and Prospects , 1991 .