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Journal of Proteome Research Oct 2023We evaluate the quantitative performance of the newly released Asymmetric Track Lossless (Astral) analyzer. Using data-independent acquisition, the Thermo Scientific...
We evaluate the quantitative performance of the newly released Asymmetric Track Lossless (Astral) analyzer. Using data-independent acquisition, the Thermo Scientific Orbitrap Astral mass spectrometer quantifies 5 times more peptides per unit time than state-of-the-art Thermo Scientific Orbitrap mass spectrometers, which have long been the gold standard for high-resolution quantitative proteomics. Our results demonstrate that the Orbitrap Astral mass spectrometer can produce high-quality quantitative measurements across a wide dynamic range. We also use a newly developed extracellular vesicle enrichment protocol to reach new depths of coverage in the plasma proteome, quantifying over 5000 plasma proteins in a 60 min gradient with the Orbitrap Astral mass spectrometer.
Topics: Proteomics; Mass Spectrometry; Peptides; Proteome; Blood Proteins
PubMed: 37683181
DOI: 10.1021/acs.jproteome.3c00357 -
Mass Spectrometry Reviews Mar 2023Advancements in liquid chromatography and mass spectrometry over the last decades have led to a significant development in mass spectrometry-based proteome... (Review)
Review
Advancements in liquid chromatography and mass spectrometry over the last decades have led to a significant development in mass spectrometry-based proteome quantification approaches. An increasingly attractive strategy is multiplex isotope labeling, which significantly improves the accuracy, precision and throughput of quantitative proteomics in the data-dependent acquisition mode. Isotope labeling-based approaches can be classified into MS1-based and MS2-based quantification. In this review, we give an overview of approaches based on chemical isotope labeling and discuss their principles, benefits, and limitations with the goal to give insights into fundamental questions and provide a useful reference for choosing a method for quantitative proteomics. As a perspective, we discuss the current possibilities and limitations of multiplex, isotope labeling approaches for the data-independent acquisition mode, which is increasing in popularity.
Topics: Proteomics; Isotope Labeling; Mass Spectrometry; Proteome; Chromatography, Liquid
PubMed: 34091937
DOI: 10.1002/mas.21709 -
Journal of the American Society For... Oct 2023Bacteria are orders of magnitude smaller than mammalian cells, and while single cell proteomics (SCP) currently detects and quantifies several thousands of proteins per...
Bacteria are orders of magnitude smaller than mammalian cells, and while single cell proteomics (SCP) currently detects and quantifies several thousands of proteins per mammalian cell, it is not clear whether conventional SCP methods will be suitable for bacteria. Here we report on the first successful attempt to detect proteins from individual bacteria, with validation of our findings by comparison with two bacteria samples and bulk proteomics data. Data are available via ProteomeXchange with the identifier PXD043473.
Topics: Bacteria; Escherichia coli; Proteome; Proteomics
PubMed: 37713396
DOI: 10.1021/jasms.3c00242 -
Molecular & Cellular Proteomics : MCP Sep 2023Data-independent acquisition (DIA) mass spectrometry-based proteomics generates reproducible proteome data. The complex processing of the DIA data has led to the...
Data-independent acquisition (DIA) mass spectrometry-based proteomics generates reproducible proteome data. The complex processing of the DIA data has led to the development of multiple data analysis tools. In this study, we assessed the performance of five tools (OpenSWATH, EncyclopeDIA, Skyline, DIA-NN, and Spectronaut) using six DIA datasets obtained from TripleTOF, Orbitrap, and TimsTOF Pro instruments. By comparing identification and quantification metrics and examining shared and unique cross-tool identifications, we evaluated both library-based and library-free approaches. Our findings indicate that library-free approaches outperformed library-based methods when the spectral library had limited comprehensiveness. However, our results also suggest that constructing a comprehensive library still offers benefits for most DIA analyses. This study provides comprehensive guidance for DIA data analysis tools, benefiting both experienced and novice users of DIA-mass spectrometry technology.
Topics: Mass Spectrometry; Proteomics; Proteome; Gene Library; Data Analysis
PubMed: 37481071
DOI: 10.1016/j.mcpro.2023.100623 -
Journal of Neurochemistry Nov 2019This Preface introduces the articles of the special issue on 'Proteomics' where we survey these powerful techniques specifically in the context of applications in...
This Preface introduces the articles of the special issue on 'Proteomics' where we survey these powerful techniques specifically in the context of applications in neurosciences. Proteomics as used here is a catch-all term for approaches where a broad survey of all protein content of a cell or tissue is performed in parallel. In the special issue, various experts outline applications as diverse as finding disease biomarkers in human samples, including living participants or post-mortem brain, as well as application of protein technologies to model systems such as animals and cells. Collectively, these articles outline the utility of current technologies for proteome interrogation and identify enhancements that will shape applications to future studies. This is the Preface for the special issue "Proteomics". Cover Image for this issue: doi: 10.1111/jnc.14530.
Topics: Brain; Humans; Neurosciences; Proteome; Proteomics
PubMed: 31625157
DOI: 10.1111/jnc.14867 -
Platelets Dec 2023Proteomics tools provide a powerful means to identify, detect, and quantify protein-related details in studies of platelet phenotype and function. Here, we consider how...
Proteomics tools provide a powerful means to identify, detect, and quantify protein-related details in studies of platelet phenotype and function. Here, we consider how historical and recent advances in proteomics approaches have informed our understanding of platelet biology, and, how proteomics tools can be used going forward to advance studies of platelets. It is now apparent that the platelet proteome is comprised of thousands of different proteins, where specific changes in platelet protein systems can accompany alterations in platelet function in health and disease. Going forward, many challenges remain in how to best carry out, validate and interpret platelet proteomics experiments. Future studies of platelet protein post-translational modifications such as glycosylation, or studies that take advantage of single cell proteomics and top-down proteomics methods all represent areas of interest to profiling and more richly understanding platelets in human wellness and disease.
Topics: Humans; Blood Platelets; Proteomics; Phenotype; Proteome
PubMed: 37246523
DOI: 10.1080/09537104.2023.2217932 -
Microbiological Research Jan 2021Proteomic approaches are being used to elucidate a better discretion of interactions occurring between host, pathogen, and/or beneficial microorganisms at the molecular... (Review)
Review
Proteomic approaches are being used to elucidate a better discretion of interactions occurring between host, pathogen, and/or beneficial microorganisms at the molecular level. Application of proteomic techniques, unravel pathogenicity, stress-related, and antioxidant proteins expressed amid plant-microbe interactions and good information have been generated. It is being perceived that a fine regulation of protein expression takes place for effective pathogen recognition, induction of resistance, and maintenance of host integrity. However, our knowledge of molecular plant-microbe interactions is still incomplete and inconsequential. This review aims to provide insight into numerous ways used for proteomic investigation including peptide/protein identification, separation, and quantification during host defense response. Here, we highlight the current progress in proteomics of defense responses elicited by bacterial, fungal, and viral pathogens in plants along with which the proteome level changes induced by beneficial microorganisms are also discussed.
Topics: Bacteria; Fungi; Host Microbial Interactions; Plant Diseases; Plant Immunity; Plant Proteins; Plants; Proteome; Proteomics
PubMed: 33022544
DOI: 10.1016/j.micres.2020.126590 -
Cell Systems Nov 2023Spatial proteomics combining microscopy-based cell phenotyping with ultrasensitive mass-spectrometry-based proteomics is an emerging and powerful concept to study cell...
Spatial proteomics combining microscopy-based cell phenotyping with ultrasensitive mass-spectrometry-based proteomics is an emerging and powerful concept to study cell function and heterogeneity in (patho)physiology. However, optimized workflows that preserve morphological information for phenotype discovery and maximize proteome coverage of few or even single cells from laser microdissected tissue are currently lacking. Here, we report a robust and scalable workflow for the proteomic analysis of ultra-low-input archival material. Benchmarking in murine liver resulted in up to 2,000 quantified proteins from single hepatocyte contours and nearly 5,000 proteins from 50-cell regions. Applied to human tonsil, we profiled 146 microregions including T and B lymphocyte niches and quantified cell-type-specific markers, cytokines, and transcription factors. These data also highlighted proteome dynamics within activated germinal centers, illuminating sites undergoing B cell proliferation and somatic hypermutation. This approach has broad implications in biomedicine, including early disease profiling and drug target and biomarker discovery. A record of this paper's transparent peer review process is included in the supplemental information.
Topics: Humans; Animals; Mice; Proteome; Proteomics; Mass Spectrometry
PubMed: 37909047
DOI: 10.1016/j.cels.2023.10.003 -
Theranostics 2022Nanostructured devices and nanoparticles have fundamentally reshaped the development of precision healthcare in recent decades. Meanwhile, mass spectrometry (MS)-based... (Review)
Review
Nanostructured devices and nanoparticles have fundamentally reshaped the development of precision healthcare in recent decades. Meanwhile, mass spectrometry (MS)-based proteomics has evolved from simple protein sequencing to a powerful approach that identifies disease patterns and signatures, reveals molecular mechanisms of pathological processes, and develops therapeutic or preventive drugs. Significantly, the two distinct disciplines have synergized and expanded our knowledge about human health and disease, as evidenced by a variety of nanotechnology-assisted sample processing strategies, facilitating in-depth proteome profiling and post-translational modifications (PTMs) characterization. This review summarizes recent advances in nanoparticle design for better enrichment of marker proteins and their PTMs from various bio-specimens and emerging nanotechnologies that are applied to MS-based proteomics for precision medicine discovery.
Topics: Humans; Mass Spectrometry; Nanostructures; Precision Medicine; Protein Processing, Post-Translational; Proteome; Proteomics
PubMed: 35401834
DOI: 10.7150/thno.64325 -
Molecular & Cellular Proteomics : MCP Jun 2023Current proteomic tools permit the high-throughput analysis of the blood proteome in large cohorts, including those enriched for chronic kidney disease (CKD) or its risk...
Current proteomic tools permit the high-throughput analysis of the blood proteome in large cohorts, including those enriched for chronic kidney disease (CKD) or its risk factors. To date, these studies have identified numerous proteins associated with cross-sectional measures of kidney function, as well as with the longitudinal risk of CKD progression. Representative signals that have emerged from the literature include an association between levels of testican-2 and favorable kidney prognosis and an association between levels of TNFRSF1A and TNFRSF1B and worse kidney prognosis. For these and other associations, however, understanding whether the proteins play a causal role in kidney disease pathogenesis remains a fundamental challenge, especially given the strong impact that kidney function can have on blood protein levels. Prior to investing in dedicated animal models or randomized trials, methods that leverage the availability of genotyping in epidemiologic cohorts-including Mendelian randomization, colocalization analyses, and proteome-wide association studies-can add evidence for causal inference in CKD proteomics research. In addition, integration of large-scale blood proteome analyses with urine and tissue proteomics, as well as improved assessment of posttranslational protein modifications (e.g., carbamylation), represent important future directions. Taken together, these approaches seek to translate progress in large-scale proteomic profiling into the promise of improved diagnostic tools and therapeutic target identification in kidney disease.
Topics: Animals; Proteome; Proteomics; Cross-Sectional Studies; Biomarkers; Renal Insufficiency, Chronic; Genome-Wide Association Study
PubMed: 37076045
DOI: 10.1016/j.mcpro.2023.100550