Review
Multidisciplinary Sciences
Lloyd M. Smith, Jeffrey N. Agar, Julia Chamot-Rooke, Paul O. Danis, Ying Ge, Joseph A. Loo, Ljiljana Pasa-Tolic, Yury O. Tsybin, Neil L. Kelleher
Summary: Understanding the structure and properties of proteins is crucial in deciphering biological functions. The concept of defining the human proteome as a reference set of proteoforms is proposed, with a call for improved technologies in a two-pronged strategy.
Article
Chemistry, Analytical
Yuming Jiang, Alexandre Hutton, Caleb W. Cranney, Jesse G. Meyer
Summary: This article introduces an improved direct infusion and ion mobility method for proteome analysis, and proposes a label-free quantification method DISPA-LFQ, which can rapidly identify and quantify proteins in complex mixtures. This technology has important applications in drug screening, biomarker discovery, and clinical analysis.
ANALYTICAL CHEMISTRY
(2022)
Review
Plant Sciences
Julia Mergner, Bernhard Kuster
Summary: Proteins play essential roles in cellular processes, and studying protein expression, interactions, and modifications is crucial for understanding the molecular mechanisms underlying plant phenotypes. Mass spectrometry technology allows for the global identification and quantification of thousands of proteins, revealing dynamic changes in the plant proteome.
ANNUAL REVIEW OF PLANT BIOLOGY
(2022)
Article
Hematology
Harriet E. Allan, Melissa A. Hayman, Simone Marcone, Melissa Chan, Matthew L. Edin, Tania Maffucci, Abhishek Joshi, Laura Menke, Marilena Crescente, Manuel Mayr, Darryl C. Zeldin, Paul C. Armstrong, Timothy D. Warner
Summary: Our study reveals that changes in protein content are associated with alterations in platelet structure and function as they age. Analysis suggests higher hemostasis in young platelets and increased apoptosis and senescence in old platelets. In-depth investigation shows reduced cytoskeletal protein, fewer mitochondria, and decreased calcium dynamics and granule secretion in aged platelets.
JOURNAL OF THROMBOSIS AND HAEMOSTASIS
(2021)
Article
Hematology
Iris C. Kreft, Elise J. Huisman, Marjon H. Cnossen, Floris P. J. van Alphen, Carmen van der Zwaan, Karin van Leeuwen, Rosalina van Spaendonk, Leendert Porcelijn, Caroline S. B. Veen, Maartje van den Biggelaar, Masja de Haas, Alexander B. Meijer, Arie J. Hoogendijk
Summary: This study profiles the platelet proteomics signatures of inherited platelet disorders (IPDs) using mass spectrometry analysis. The results demonstrate the extensive proteomic alterations caused by different genetic variants, providing insights into the biology of platelet (dys)function.
JOURNAL OF THROMBOSIS AND HAEMOSTASIS
(2023)
Article
Chemistry, Analytical
R. Rola, K. Kowalski, T. Bienkowski, J. Witwicki, S. Studzinska
Summary: The study demonstrated the utility of DBS samples in assessing newborns' vitamin D levels, comparing them to maternal and cord blood-derived serum tests. Results showed that DBS could be used interchangeably with cord blood-derived serum to determine vitamin D status in neonates, simplifying the screening process.
MICROCHEMICAL JOURNAL
(2021)
Article
Chemistry, Analytical
D. Alex Crowder, Vladimir Sarpe, Bruno C. Amaral, Nicholas I. Brodie, Andrew R. M. Michael, David C. Schriemer
Summary: Crosslinking mass spectrometry (XL-MS) is a valuable technique for measuring distances in protein space, but efficient software is needed for cell-based XL-MS experiments. A new scoring method called CRIMP 2.0 is presented, which uses a rapid presearch method and computer vision-inspired concept to detect crosslinked peptides with high sensitivity. The method demonstrates high crosslink detection rates and can efficiently complete complex proteome-level searches on a conventional desktop computer.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Lukasz Pawel Kozlowski
Summary: Proteome-pI 2.0 is an online database that predicts the isoelectric points and pKa values of proteins and peptides, catering to analytical biochemistry and proteomics techniques. The database includes over 61 million protein sequences and utilizes 21 methods to predict the isoelectric point of proteins and one method for inferring pKa values, facilitating bottom-up proteomics analysis.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Lin Bai, Guojian Yang, Zhaoyu Qin, Jiacheng Lyu, Yunzhi Wang, Jinwen Feng, Mingwei Liu, Tongqing Gong, Xianju Li, Zhengyang Li, Jixi Li, Jun Qin, Wenjun Yang, Chen Ding
Summary: This study used a novel method to analyze the binding activity of transcription factors under DNA modifications and identified potential readers for 5fC-modified DNA. By quantifying the modified DNA-binding activity of 1039 TFs, it revealed the hierarchical networks between the transcriptional protein machinery and modified DNA.
Article
Chemistry, Analytical
Carolina Rojas Ramirez, Jessica A. Espino, Lisa M. Jones, Daniel A. Polasky, Alexey I. Nesvizhskii
Summary: Monitoring protein structure before and after environmental alterations can provide insights into protein function. Fast photochemical oxidation of proteins (FPOP) coupled with mass spectrometry allows for monitoring of structural rearrangements by exposing proteins to radicals. However, the challenges of processing FPOP data have limited its proteome-scale uses. In this study, a computational workflow was developed to analyze FPOP data sets more efficiently, enabling the identification of modified peptide spectra at a faster rate than previous methods.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Ayako Takemori, Philipp T. Kaulich, Liam Cassidy, Nobuaki Takemori, Andreas Tholey
Summary: The combination of liquid chromatography (LC) and gas-phase separation by field-asymmetric ion mobility spectrometry (FAIMS) is a powerful proteoform separation system for top-down proteomics. In this study, an in-depth top-down proteomics workflow, GeLC-FAIMS-MS, was presented, which utilized a molecular-weight-based proteome fractionation approach using SDS-poly-acrylamide gel electrophoresis. The authors optimized the MS parameters for each gel band and compensating voltage (CV) to improve the identification of proteoforms. They also developed a simple and cost-effective method, combining the PEPPI protocol with an AnExSP method, for stain and SDS removal. Results showed that this method was better suited for low-molecular-weight proteoforms, while a methanol-chloroform-water (MCW)-based protocol showed advantages for higher-molecular-weight proteoforms.
ANALYTICAL CHEMISTRY
(2022)
Article
Biology
Jonathan G. Van Vranken, Jiaming Li, Dylan C. Mitchell, Jose Navarrete-Perea, Steven P. Gygi
Summary: Recent advances in mass spectrometry have enabled quantitative proteomics to become a powerful tool in drug discovery, with the development of solvent shift assays allowing for the establishment of target engagement and increased efficiency. Using this approach, specific targets of compounds with known mechanisms of action can be readily identified, and combining solvent proteome profiling with other methods can expand the screening capabilities for evidence of ligand binding in the proteome.
Article
Multidisciplinary Sciences
V. Dumrongprechachan, R. B. Salisbury, G. Soto, M. Kumar, M. L. MacDonald, Y. Kozorovitskiy
Summary: This study employed a genetically targeted APEX2-based proximity labeling approach to uncover proteome dynamics in two classes of striatal spiny projection neurons in the mouse brain. The findings were validated using imaging, electron microscopy, and mass spectrometry, providing important insights for understanding the development and functional organization of neural circuits in the brain.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Yanmei Chen, Yi Wang, Jun Yang, Wenbin Zhou, Shaojun Dai
Summary: This paper reviews recent breakthroughs and strategies in unraveling the diversity of the plant proteome, focusing on the methods used to analyze posttranslational modifications (PTMs), protein localization, and the organization of proteins into functional modules. It also discusses PTM crosstalk, multiple PTMs temporally regulating protein life cycles, quantitative studies using MS to measure protein turnover rates, and future directions in the study of the plant proteome.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Article
Biochemical Research Methods
Florian A. Rosenberger, Marvin Thielert, Maximilian T. Strauss, Lisa Schweizer, Constantin Ammar, Sophia C. Maedler, Andreas Metousis, Patricia Skowronek, Maria Wahle, Katherine Madden, Janine Gote-Schniering, Anna Semenova, Herbert B. Schiller, Edwin Rodriguez, Thierry M. Nordmann, Andreas Mund, Matthias Mann
Summary: Single-cell proteomics by mass spectrometry is a powerful method for studying biological heterogeneity, and single-cell Deep Visual Proteomics (scDVP) is a technology that integrates high-content imaging, laser microdissection, and multiplexed mass spectrometry to analyze the spatial proteome of tissues. It can identify thousands of proteins and reveal differential regulation in spatially distinct regions.
Article
Hematology
Maaike Schillemans, Ellie Karampini, Bart L. van den Eshof, Anastasia Gangaev, Menno Hofman, Dorothee van Breevoort, Henriet Meems, Hans Janssen, Aat A. Mulder, Carolina R. Jost, Johanna C. Escher, Ruediger Adam, Tom Carter, Abraham J. Koster, Maartje van den Biggelaar, Jan Voorberg, Ruben Bierings
ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY
(2018)
Article
Hematology
Maartje van den Biggelaar, Juan Ramon Hernandez-Fernaud, Bart L. van den Eshof, Lisa J. Neilson, Alexander B. Meijer, Koen Mertens, Sara Zanivan
Article
Multidisciplinary Sciences
Maaike Rijkers, Bart L. van den Eshof, Pieter F. van der Meer, Floris P. J. van Alphen, Dirk de Korte, Frank W. G. Leebeek, Alexander B. Meijer, Jan Voorberg, A. J. Gerard Jansen
SCIENTIFIC REPORTS
(2017)
Article
Biochemistry & Molecular Biology
Thierry Schmidlin, Donna O. Debets, Charlotte A. G. H. van Gelder, Kelly E. Stecker, Stamatia Rontogianni, Bart L. van den Eshof, Kristel Kemper, Esther H. Lips, Maartje van den Biggelaar, Daniel S. Peeper, Albert J. R. Heck, Maarten Altelaar
Review
Cell Biology
Bart L. van den Eshof, Lobna Medfai, Emanuele Nolfi, Magdalena Wawrzyniuk, Alice J. A. M. Sijts
Summary: Immunoproteasomes are a specialized form of proteasomes assembled by immune system cells, with cytokine-inducible homologues replacing constitutive catalytic sites. They are adapted for MHC class I antigen processing and CD8(+) T-cell activation, potentially contributing to both CD8(+) T-cell-mediated control of intracellular infections and the immunopathogenesis of autoimmune diseases.
Article
Biology
Stijn A. Groten, Eva R. Smit, Esmee F. J. Janssen, Bart L. van den Eshof, Floris P. J. van Alphen, Carmen van der Zwaan, Alexander B. Meijer, Arie J. Hoogendijk, Maartje van den Biggelaar
Summary: Vascular endothelial cells play a crucial role in vascular inflammation, and TNF alpha and IFN gamma induce the largest response in these cells, resulting in distinct proteomic inflammatory signatures. Moreover, the combined stimulation of TNF alpha + IFN gamma leads to a synergistic inflammatory signature.
COMMUNICATIONS BIOLOGY
(2023)
Article
Hematology
Bart L. van den Eshof, Arie J. Hoogendijk, Pelle J. Simpson, Floris P. J. van Alphen, Sara Zanivan, Koen Mertens, Alexander B. Meijer, Maartje van den Biggelaar
ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY
(2017)
