ACS Publications. Most Trusted. Most Cited. Most Read
My Activity

Figure 1Loading Img

Extending the Compatibility of the SP3 Paramagnetic Bead Processing Approach for Proteomics

  • Sophie Moggridge
    Sophie Moggridge
    Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
    Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3E6, Canada
  • Poul H. Sorensen
    Poul H. Sorensen
    Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada
  • Gregg B. Morin*
    Gregg B. Morin
    Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
    Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
    *E-mail: [email protected]
  • , and 
  • Christopher S. Hughes
    Christopher S. Hughes
    Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
Cite this: J. Proteome Res. 2018, 17, 4, 1730–1740
Publication Date (Web):March 22, 2018
Copyright © 2018 American Chemical Society

    Article Views





    Other access options
    Supporting Info (2)»


    Abstract Image

    The diversity in protein and peptide biochemistry necessitates robust protocols and reagents for efficiently handling and enriching these molecules prior to analysis with mass spectrometry (MS) or other techniques. Further exploration of the paramagnetic bead-based approach, single-pot solid-phase-enhanced sample preparation (SP3), is carried out toward updating and extending previously described conditions and experimental workflows. The SP3 approach was tested in a wide range of experimental scenarios, including (1) binding solvents (acetonitrile, ethanol, isopropanol, acetone), (2) binding pH (acidic vs neutral), (3) solvent/lysate ratios (50–200%, v/v), (4) mixing and rinsing conditions (on-rack vs off-rack rinsing), (5) Enrichment of nondenatured proteins, and (6) capture of individual proteins from noncomplex mixtures. These results highlight the robust handling of proteins in a broad set of scenarios while also enabling the development of a modified SP3 workflow that offers extended compatibility. The modified SP3 approach is used in quantitative in-depth proteome analyses to compare it with commercial paramagnetic bead-based HILIC methods (MagReSyn) and across multiple binding conditions (e.g., pH and solvent during binding). Together, these data reveal the extensive quantitative coverage of the proteome possible with SP3 independent of the binding approach utilized. The results further establish the utility of SP3 for the unbiased handling of peptides and proteins for proteomic applications.

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.


    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. You can change your affiliated institution below.

    Supporting Information

    Jump To

    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jproteome.7b00913.

    • Figures S-1 and S-2. Handling of protein mixtures with SP3 using a variety of solvents. Figures S-3–S-6. Processing of proteins using SP3 with modified mixing and rinsing approaches. Figures S-7 and S-8. Measurement of reproducibility between SP3 batches and technical replicates. Figure S-9. Processing of nondenatured proteins with SP3. Figure S-10. Processing of noncomplex protein mixtures with SP3. Figure S-11. Identifications overlap in the in-depth proteome analysis of samples processed with SP3. (PDF)

    • Tables S-1 and S-2. Whole-proteome analysis of SP3 in comparison with MagReSyn and across different processing conditions. (XLSX)

    Terms & Conditions

    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system:

    Cited By

    This article is cited by 145 publications.

    1. Anna-Lena Mayr, Karin Hummel, David Leitsch, Ebrahim Razzazi-Fazeli. A Comparison of Bottom-Up Proteomic Sample Preparation Methods for the Human Parasite Trichomonas vaginalis. ACS Omega 2024, 9 (8) , 9782-9791.
    2. Dylan Z. Dieters-Castator, Paolo Manzanillo, Han-Yin Yang, Rucha V. Modak, Matthew J. Rardin, Bradford W. Gibson. Magnetic Bead-Based Workflow for Sensitive and Streamlined Cell Surface Proteomics. Journal of Proteome Research 2024, 23 (2) , 618-632.
    3. Yi-Kai Liu, Xiaofeng Wu, Marco Hadisurya, Li Li, Hristos Kaimakliotis, Anton Iliuk, W. Andy Tao. One-Pot Analytical Pipeline for Efficient and Sensitive Proteomic Analysis of Extracellular Vesicles. Journal of Proteome Research 2023, 22 (10) , 3301-3310.
    4. Laura K. Muehlbauer, Annie Jen, Yunyun Zhu, Yuchen He, Evgenia Shishkova, Katherine A. Overmyer, Joshua J. Coon. Rapid Multi-Omics Sample Preparation for Mass Spectrometry. Analytical Chemistry 2023, 95 (2) , 659-667.
    5. Lynda Agbo, Jérémy Loehr, Pata-Eting Kougnassoukou Tchara, Jean-Philippe Lambert. Characterization of the Functional Interplay between the BRD7 and BRD9 Homologues in mSWI/SNF Complexes. Journal of Proteome Research 2023, 22 (1) , 78-90.
    6. Vinayak Singh, Anna E. Grzegorzewicz, Stephen Fienberg, Rudolf Müller, Lutete Peguy Khonde, Olalla Sanz, Salvatore Alfonso, Beatriz Urones, Gerard Drewes, Marcus Bantscheff, Sonja Ghidelli-Disse, Thomas R. Ioerger, Bhanupriya Angala, Jiuyu Liu, Richard E. Lee, James C. Sacchettini, Inna V. Krieger, Mary Jackson, Kelly Chibale, Sandeep R. Ghorpade. 1,3-Diarylpyrazolyl-acylsulfonamides Target HadAB/BC Complex in Mycobacterium tuberculosis. ACS Infectious Diseases 2022, 8 (11) , 2315-2326.
    7. Harvey E. Johnston, Kranthikumar Yadav, Joanna M. Kirkpatrick, George S. Biggs, David Oxley, Holger B. Kramer, Rahul S. Samant. Solvent Precipitation SP3 (SP4) Enhances Recovery for Proteomics Sample Preparation without Magnetic Beads. Analytical Chemistry 2022, 94 (29) , 10320-10328.
    8. Matthew R. McIlvin, Mak A. Saito. Online Nanoflow Two-Dimension Comprehensive Active Modulation Reversed Phase–Reversed Phase Liquid Chromatography High-Resolution Mass Spectrometry for Metaproteomics of Environmental and Microbiome Samples. Journal of Proteome Research 2021, 20 (9) , 4589-4597.
    9. Zhijun Cao, Daniel T. Sloper, Noriko Nakamura. Identification of Altered Proteins in the Plasma of Rats With Chronic Prostatic Inflammation Induced by Estradiol Benzoate and Sex Hormones. ACS Omega 2021, 6 (22) , 14361-14370.
    10. Xinyue Liu, Steven P. Gygi, Joao A. Paulo. A Semiautomated Paramagnetic Bead-Based Platform for Isobaric Tag Sample Preparation. Journal of the American Society for Mass Spectrometry 2021, 32 (6) , 1519-1529.
    11. Karren S. Palmer, Cheryl A. Makarewicz, Alexey A. Tishkin, Svetlana S. Tur, Amartuvshin Chunag, Erdenebaatar Diimajav, Bayarsaikhan Jamsranjav, Michael Buckley. Comparing the Use of Magnetic Beads with Ultrafiltration for Ancient Dental Calculus Proteomics. Journal of Proteome Research 2021, 20 (3) , 1689-1704.
    12. Nico Zinn, Thilo Werner, Carola Doce, Toby Mathieson, Christine Boecker, Gavain Sweetman, Christian Fufezan, Marcus Bantscheff. Improved Proteomics-Based Drug Mechanism-of-Action Studies Using 16-Plex Isobaric Mass Tags. Journal of Proteome Research 2021, 20 (3) , 1792-1801.
    13. Aleksandr Gaun, Kaitlyn N. Lewis Hardell, Niclas Olsson, Jonathon J. O’Brien, Sudha Gollapudi, Megan Smith, Graeme McAlister, Romain Huguet, Robert Keyser, Rochelle Buffenstein, Fiona E. McAllister. Automated 16-Plex Plasma Proteomics with Real-Time Search and Ion Mobility Mass Spectrometry Enables Large-Scale Profiling in Naked Mole-Rats and Mice. Journal of Proteome Research 2021, 20 (2) , 1280-1295.
    14. Pascal Steffen, Jun Li, Jason Chandra, Mahsa S. Ahadi, Anthony J. Gill, Alexander F. Engel, Mark P. Molloy. Molecular Features of Lymph Node Metastasis in T1/2 Colorectal Cancer from Formalin-Fixed Paraffin-Embedded Archival Specimens. Journal of Proteome Research 2021, 20 (2) , 1304-1312.
    15. Malin Källsten, Mohan Ghorasaini, Rafael Hartmann, Fredrik Lehmann, Jonas Bergquist, Lucia Kovac, Sara Bergström Lind. Magnetic Beads for Desalting of Monoclonal Antibodies and Antibody–Drug Conjugates. Analytical Chemistry 2020, 92 (13) , 9001-9007.
    16. Lucia F. Zacchi, Dinora Roche Recinos, Ellen Otte, Campbell Aitken, Tony Hunt, Vanessa Sandford, Yih Yean Lee, Benjamin L. Schulz, Christopher B. Howard. S-Trap Eliminates Cell Culture Media Polymeric Surfactants for Effective Proteomic Analysis of Mammalian Cell Bioreactor Supernatants. Journal of Proteome Research 2020, 19 (5) , 2149-2158.
    17. Teresa Mendes Maia, An Staes, Kim Plasman, Jarne Pauwels, Katie Boucher, Andrea Argentini, Lennart Martens, Tony Montoye, Kris Gevaert, Francis Impens. Simple Peptide Quantification Approach for MS-Based Proteomics Quality Control. ACS Omega 2020, 5 (12) , 6754-6762.
    18. Dimitrios Lampaki, Andreas Diepold, Timo Glatter. A Serial Sample Processing Strategy with Improved Performance for in-Depth Quantitative Analysis of Type III Secretion Events in Pseudomonas aeruginosa. Journal of Proteome Research 2020, 19 (1) , 543-553.
    19. Alexios N. Matralis, Adnan Malik, Maria Penzo, Inmaculada Moreno, Maria J. Almela, Isabel Camino, Benigno Crespo, Anas Saadeddin, Sonja Ghidelli-Disse, Lourdes Rueda, Felix Calderon, Simon A. Osborne, Gerard Drewes, Markus Böesche, Elena Fernández-Álvaro, Jose Ignacio Martin Hernando, David A. Baker. Development of Chemical Entities Endowed with Potent Fast-Killing Properties against Plasmodium falciparum Malaria Parasites. Journal of Medicinal Chemistry 2019, 62 (20) , 9217-9235.
    20. Laura F. Dagley, Giuseppe Infusini, Rune H. Larsen, Jarrod J. Sandow, Andrew I. Webb. Universal Solid-Phase Protein Preparation (USP3) for Bottom-up and Top-down Proteomics. Journal of Proteome Research 2019, 18 (7) , 2915-2924.
    21. Matthew Waas, Michael Pereckas, Rachel A. Jones Lipinski, Christopher Ashwood, Rebekah L. Gundry. SP2: Rapid and Automatable Contaminant Removal from Peptide Samples for Proteomic Analyses. Journal of Proteome Research 2019, 18 (4) , 1644-1656.
    22. Timothy P. Cleland. Human Bone Paleoproteomics Utilizing the Single-Pot, Solid-Phase-Enhanced Sample Preparation Method to Maximize Detected Proteins and Reduce Humics. Journal of Proteome Research 2018, 17 (11) , 3976-3983.
    23. Kevin A. Kovalchik, Sophie Moggridge, David D. Y. Chen, Gregg B. Morin, Christopher S. Hughes. Parsing and Quantification of Raw Orbitrap Mass Spectrometer Data Using RawQuant. Journal of Proteome Research 2018, 17 (6) , 2237-2247.
    24. Verena Kohler, Andreas Kohler, Lisa Larsson Berglund, Xinxin Hao, Sarah Gersing, Axel Imhof, Thomas Nyström, Johanna L. Höög, Martin Ott, Claes Andréasson, Sabrina Büttner. Nuclear Hsp104 safeguards the dormant translation machinery during quiescence. Nature Communications 2024, 15 (1)
    25. Nona Struyf, Albin Österroos, Mattias Vesterlund, Cornelia Arnroth, Tojo James, Stephanie Sunandar, Georgios Mermelekas, Anna Bohlin, Kerstin Hamberg Levedahl, Sofia Bengtzén, Rozbeh Jafari, Lukas M. Orre, Janne Lehtiö, Sören Lehmann, Päivi Östling, Olli Kallioniemi, Brinton Seashore-Ludlow, Tom Erkers. Delineating functional and molecular impact of ex vivo sample handling in precision medicine. npj Precision Oncology 2024, 8 (1)
    26. Panagiotis Papoutsoglou, Raphaël Pineau, Raffaële Leroux, Corentin Louis, Anaïs L’Haridon, Dominika Foretek, Antonin Morillon, Jesus M Banales, David Gilot, Marc Aubry, Cédric Coulouarn. TGFβ-induced long non-coding RNA LINC00313 activates Wnt signaling and promotes cholangiocarcinoma. EMBO Reports 2024, 29
    27. Chloé Jacquemin, Nicolas Villain, Rita Azevedo, Susana Boluda, Etienne A. Thévenot, François Fenaille, Foudil Lamari, François Becher. Evaluation of SP3 for antibody-free quantification of tau in CSF mimic and brain by mass spectrometry. European Journal of Mass Spectrometry 2024, 30 (1) , 65-75.
    28. Desirée Martín-García, Marilina García-Aranda, Maximino Redondo. Biomarker Identification through Proteomics in Colorectal Cancer. International Journal of Molecular Sciences 2024, 25 (4) , 2283.
    29. Pedro L. Moura, Teresa Mortera-Blanco, Isabel J. Hofman, Gabriele Todisco, Warren W. Kretzschmar, Ann-Charlotte Björklund, Maria Creignou, Michael Hagemann-Jensen, Christoph Ziegenhain, David Cabrerizo Granados, Indira Barbosa, Gunilla Walldin, Monika Jansson, Neil Ashley, Adam J. Mead, Vanessa Lundin, Marios Dimitriou, Tetsuichi Yoshizato, Petter S. Woll, Seishi Ogawa, Rickard Sandberg, Sten Eirik W. Jacobsen, Eva Hellström-Lindberg. Erythroid Differentiation Enhances RNA Mis-Splicing in SF3B1 -Mutant Myelodysplastic Syndromes with Ring Sideroblasts. Cancer Research 2024, 84 (2) , 211-225.
    30. Yong-Er Wang, Wei-Lan Zeng, Sheng-Tian Cao, Jun-Peng Zou, Cui-Ting Liu, Jun-Min Shi, Jing Li, Feng Qiu, Yan Wang. Development of a sample preparation method for micro-proteomics analysis of the formaldehyde-fixed paraffin-embedded liver tissue samples. Talanta 2024, 266 , 125106.
    31. Eric B. Emanuelsson, Muhammad Arif, Stefan M. Reitzner, Sean Perez, Maléne E. Lindholm, Adil Mardinoglu, Carsten Daub, Carl Johan Sundberg, Mark A. Chapman. Remodeling of the human skeletal muscle proteome found after long-term endurance training but not after strength training. iScience 2024, 27 (1) , 108638.
    32. Josh McQuail, Gianluca Matera, Tom Gräfenhan, Thorsten Bischler, Per Haberkant, Frank Stein, Jörg Vogel, Sivaramesh Wigneshweraraj. Global Hfq-mediated RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery. Nucleic Acids Research 2023, 9
    33. Komal Soni, Anusree Sivadas, Attila Horvath, Nikolay Dobrev, Rippei Hayashi, Leo Kiss, Bernd Simon, Klemens Wild, Irmgard Sinning, Tamás Fischer. Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex. Nature Communications 2023, 14 (1)
    34. Ioannis Skalidis, Fotis L. Kyrilis, Christian Tüting, Farzad Hamdi, Toni K. Träger, Jaydeep Belapure, Gerd Hause, Marta Fratini, Francis J. O’Reilly, Ingo Heilmann, Juri Rappsilber, Panagiotis L. Kastritis. Structural analysis of an endogenous 4-megadalton succinyl-CoA-generating metabolon. Communications Biology 2023, 6 (1)
    35. Marieke Theodora Roefs, Julia Bauzá-Martinez, Simonides Immanuel van de Wakker, Jiabin Qin, Willem Theodoor Olijve, Robin Tuinte, Marjolein Rozeboom, Christian Snijders Blok, Emma Alise Mol, Wei Wu, Pieter Vader, Joost Petrus Gerardus Sluijter. Cardiac progenitor cell-derived extracellular vesicles promote angiogenesis through both associated- and co-isolated proteins. Communications Biology 2023, 6 (1)
    36. Haris Babačić, Wanda Christ, José Eduardo Araújo, Georgios Mermelekas, Nidhi Sharma, Janne Tynell, Marina García, Renata Varnaite, Hilmir Asgeirsson, Hedvig Glans, Janne Lehtiö, Sara Gredmark-Russ, Jonas Klingström, Maria Pernemalm. Comprehensive proteomics and meta-analysis of COVID-19 host response. Nature Communications 2023, 14 (1)
    37. Nikolai Juul, Oliver Willacy, Doste R. Mamand, Samir El Andaloussi, Jesper Eisfeldt, Clara I. Chamorro, Magdalena Fossum. Insights into cellular behavior and micromolecular communication in urothelial micrografts. Scientific Reports 2023, 13 (1)
    38. Björn E. Clausen, Lukas Amon, Ronald A. Backer, Luciana Berod, Tobias Bopp, Anna Brand, Sven Burgdorf, Luxia Chen, Meihong Da, Ute Distler, Regine J. Dress, Diana Dudziak, Charles‐Antoine Dutertre, Christina Eich, Anna Gabele, Melanie Geiger, Florent Ginhoux, Lucila Giusiano, Gloria J. Godoy, Ahmed E.I. Hamouda, Lukas Hatscher, Lukas Heger, Gordon F. Heidkamp, Lola C. Hernandez, Lukas Jacobi, Tomasz Kaszubowski, Wan Ting Kong, Christian H. K. Lehmann, Tamara López‐López, Karsten Mahnke, Dominik Nitsche, Jörg Renkawitz, Rifat A. Reza, Pablo J. Sáez, Laura Schlautmann, Madeleine T. Schmitt, Anna Seichter, Malte Sielaff, Tim Sparwasser, Patrizia Stoitzner, Giorgi Tchitashvili, Stefan Tenzer, Nounagnon R. Tochoedo, Damir Vurnek, Fabian Zink, Thomas Hieronymus. Guidelines for mouse and human DC functional assays. European Journal of Immunology 2023, 53 (12)
    39. Andrä Brunner, Qiuzhen Li, Samuele Fisicaro, Alexandros Kourtesakis, Johanna Viiliäinen, Henrik J. Johansson, Vijaya Pandey, Adarsh K. Mayank, Janne Lehtiö, James A. Wohlschlegel, Charles Spruck, Juha K. Rantala, Lukas M. Orre, Olle Sangfelt. FBXL12 degrades FANCD2 to regulate replication recovery and promote cancer cell survival under conditions of replication stress. Molecular Cell 2023, 83 (20) , 3720-3739.e8.
    40. Oliver J. Ziff, Jasmine Harley, Yiran Wang, Jacob Neeves, Giulia Tyzack, Fairouz Ibrahim, Mark Skehel, Anob M. Chakrabarti, Gavin Kelly, Rickie Patani. Nucleocytoplasmic mRNA redistribution accompanies RNA binding protein mislocalization in ALS motor neurons and is restored by VCP ATPase inhibition. Neuron 2023, 111 (19) , 3011-3027.e7.
    41. Eduardo Alvarez-Rivera, Emanuel J. Ortiz-Hernández, Elyette Lugo, Lorraine M. Lozada-Reyes, Nawal M. Boukli. Oncogenic Proteomics Approaches for Translational Research and HIV-Associated Malignancy Mechanisms. Proteomes 2023, 11 (3) , 22.
    42. Clément Boussardon, Chris Carrie, Olivier Keech, . Comparison of plastid proteomes points towards a higher plastidial redox turnover in vascular tissues than in mesophyll cells. Journal of Experimental Botany 2023, 74 (14) , 4110-4124.
    43. Sarah C. Erlandson, Shaun Rawson, James Osei-Owusu, Kelly P. Brock, Xinyue Liu, Joao A. Paulo, Julian Mintseris, Steven P. Gygi, Debora S. Marks, Xiaojing Cong, Andrew C. Kruse. The relaxin receptor RXFP1 signals through a mechanism of autoinhibition. Nature Chemical Biology 2023, 19 (8) , 1013-1021.
    44. Rabea J. Madel, Verena Börger, Robin Dittrich, Michel Bremer, Tobias Tertel, Nhi Ngo Thi Phuong, Hideo A. Baba, Lambros Kordelas, Simon Staubach, Frank Stein, Per Haberkant, Matthias Hackl, Regina Grillari, Johannes Grillari, Jan Buer, Peter A. Horn, Astrid M. Westendorf, Sven Brandau, Carsten J. Kirschning, Bernd Giebel. Independent human mesenchymal stromal cell–derived extracellular vesicle preparations differentially attenuate symptoms in an advanced murine graft-versus-host disease model. Cytotherapy 2023, 25 (8) , 821-836.
    45. Cody R. Marshall, Melissa A. Farrow, Katerina V. Djambazova, Jeffrey M. Spraggins. Untangling Alzheimer’s disease with spatial multi-omics: a brief review. Frontiers in Aging Neuroscience 2023, 15
    46. Yuanyuan Zhang, Yumeng Zhang, Evelyn Hutterer, Sara Hultin, Otto Bergman, Solrun Kolbeinsdottir, Hong Jin, Maria J. Forteza, Daniel F. J. Ketelhuth, Joy Roy, Ulf Hedin, Martin Enge, Ljubica Matic, Per Eriksson, Lars Holmgren. The VE-cadherin/AmotL2 mechanosensory pathway suppresses aortic inflammation and the formation of abdominal aortic aneurysms. Nature Cardiovascular Research 2023, 2 (7) , 629-644.
    47. Sihem Hannat, Issam Hasni, Philippe Decloquement, Seydina Diene, Saïd Azza, Bernard La Scola, Sarah Aherfi. Proteomics of the Oomycete Phytophthora parasitica Strain INRA 310. Crops 2023, 3 (2) , 116-123.
    48. Carina Groh, Per Haberkant, Frank Stein, Sebastian Filbeck, Stefan Pfeffer, Mikhail M Savitski, Felix Boos, Johannes M Herrmann. Mitochondrial dysfunction rapidly modulates the abundance and thermal stability of cellular proteins. Life Science Alliance 2023, 6 (6) , e202201805.
    49. Aušra Nemeikaitė-Čėnienė, Per Haberkant, Dalius Kučiauskas, Frank Stein, Narimantas Čėnas. Redox Proteomic Profile of Tirapazamine-Resistant Murine Hepatoma Cells. International Journal of Molecular Sciences 2023, 24 (7) , 6863.
    50. Svea Stratmann, Mattias Vesterlund, Husen M. Umer, Saeed Eshtad, Aron Skaftason, Morten Krogh Herlin, Christer Sundström, Anna Eriksson, Martin Höglund, Josefine Palle, Jonas Abrahamsson, Kirsi Jahnukainen, Monica Cheng Munthe-Kaas, Bernward Zeller, Katja Pokrovskaja Tamm, Cecilia Lindskog, Lucia Cavelier, Janne Lehtiö, Linda Holmfeldt. Proteogenomic analysis of acute myeloid leukemia associates relapsed disease with reprogrammed energy metabolism both in adults and children. Leukemia 2023, 37 (3) , 550-559.
    51. Lennart Schada von Borzyskowski, Helena Schulz-Mirbach, Mauricio Troncoso Castellanos, Francesca Severi, Paul A. Gómez-Coronado, Nicole Paczia, Timo Glatter, Arren Bar-Even, Steffen N. Lindner, Tobias J. Erb. Implementation of the β-hydroxyaspartate cycle increases growth performance of Pseudomonas putida on the PET monomer ethylene glycol. Metabolic Engineering 2023, 76 , 97-109.
    52. Ekenedirichukwu N. Obi, Daniel A. Tellock, Gabriel J. Thomas, Timothy D. Veenstra. Biomarker Analysis of Formalin-Fixed Paraffin-Embedded Clinical Tissues Using Proteomics. Biomolecules 2023, 13 (1) , 96.
    53. Paula Carrillo-Rodriguez, Frode Selheim, Maria Hernandez-Valladares. Mass Spectrometry-Based Proteomics Workflows in Cancer Research: The Relevance of Choosing the Right Steps. Cancers 2023, 15 (2) , 555.
    54. Laura Guantay, Cintia Garro, Sebastián Siri, María Florencia Pansa, Sonja Ghidelli-Disse, Natalia Paviolo, Ana Racca, Viviana Nicotra, Caius Radu, José Luis Bocco, Rosana Felice, Keith H Jansson, Katja Remlinger, Alejandro Amador, Euan Stronach, Kevin Coleman, Marcel Muelbaier, Gerard Drewes, Isro Gloger, Kevin Madauss, Manuela García, Vanesa Gottifredi, Gastón Soria. Deoxycytidine kinase (dCK) inhibition is synthetic lethal with BRCA2 deficiency. Drug Resistance Updates 2023, 18 , 100932.
    55. Karama Asleh, Nazia Riaz, Torsten O. Nielsen. Heterogeneity of triple negative breast cancer: Current advances in subtyping and treatment implications. Journal of Experimental & Clinical Cancer Research 2022, 41 (1)
    56. Jutta Diessl, Jens Berndtsson, Filomena Broeskamp, Lukas Habernig, Verena Kohler, Carmela Vazquez-Calvo, Arpita Nandy, Carlotta Peselj, Sofia Drobysheva, Ludovic Pelosi, F.-Nora Vögtle, Fabien Pierrel, Martin Ott, Sabrina Büttner. Manganese-driven CoQ deficiency. Nature Communications 2022, 13 (1)
    57. Sophie A. Herbst, Mattias Vesterlund, Alexander J. Helmboldt, Rozbeh Jafari, Ioannis Siavelis, Matthias Stahl, Eva C. Schitter, Nora Liebers, Berit J. Brinkmann, Felix Czernilofsky, Tobias Roider, Peter-Martin Bruch, Murat Iskar, Adam Kittai, Ying Huang, Junyan Lu, Sarah Richter, Georgios Mermelekas, Husen Muhammad Umer, Mareike Knoll, Carolin Kolb, Angela Lenze, Xiaofang Cao, Cecilia Österholm, Linus Wahnschaffe, Carmen Herling, Sebastian Scheinost, Matthias Ganzinger, Larry Mansouri, Katharina Kriegsmann, Mark Kriegsmann, Simon Anders, Marc Zapatka, Giovanni Del Poeta, Antonella Zucchetto, Riccardo Bomben, Valter Gattei, Peter Dreger, Jennifer Woyach, Marco Herling, Carsten Müller-Tidow, Richard Rosenquist, Stephan Stilgenbauer, Thorsten Zenz, Wolfgang Huber, Eugen Tausch, Janne Lehtiö, Sascha Dietrich. Proteogenomics refines the molecular classification of chronic lymphocytic leukemia. Nature Communications 2022, 13 (1)
    58. Emmanouela Kallergi, Akrivi-Dimitra Daskalaki, Angeliki Kolaxi, Come Camus, Evangelia Ioannou, Valentina Mercaldo, Per Haberkant, Frank Stein, Kyriaki Sidiropoulou, Yannis Dalezios, Mikhail M. Savitski, Claudia Bagni, Daniel Choquet, Eric Hosy, Vassiliki Nikoletopoulou. Dendritic autophagy degrades postsynaptic proteins and is required for long-term synaptic depression in mice. Nature Communications 2022, 13 (1)
    59. Karama Asleh, Gian Luca Negri, Sandra E. Spencer Miko, Shane Colborne, Christopher S. Hughes, Xiu Q. Wang, Dongxia Gao, C. Blake Gilks, Stephen K. L. Chia, Torsten O. Nielsen, Gregg B. Morin. Proteomic analysis of archival breast cancer clinical specimens identifies biological subtypes with distinct survival outcomes. Nature Communications 2022, 13 (1)
    60. Chris Kedong Wang, Irina Nelepcu, Desmond Hui, Htoo Zarni Oo, Sarah Truong, Sarah Zhao, Zakir Tahiry, Shaghayegh Esfandnia, Fariba Ghaidi, Hans Adomat, Robert Dagil, Tobias Gustavsson, Swati Choudhary, Ali Salanti, Poul H. Sorensen, Nader Al Nakouzi, Mads Daugaard. Internalization and trafficking of CSPG-bound recombinant VAR2CSA lectins in cancer cells. Scientific Reports 2022, 12 (1)
    61. Eleni Dalaka, Demetrios Vassilakos, Georgios C. Stefos, Aphrodite I. Kalogianni, Irida Palamidi, Athanasios I. Gelasakis, Ioannis Politis, Georgios Theodorou. Utilization of 2D and 3D cell cultures for the modelling of intramammary infection in sheep. Frontiers in Animal Science 2022, 3
    62. Kidon Sung, Miseon Park, Jungwhan Chon, Ohgew Kweon, Saeed A. Khan, Andrew Shen, Angel Paredes. Concentration-Dependent Global Quantitative Proteome Response of Staphylococcus epidermidis RP62A Biofilms to Subinhibitory Tigecycline. Cells 2022, 11 (21) , 3488.
    63. Katerina Danko, Elena Lukasheva, Vladimir A. Zhukov, Viktor Zgoda, Andrej Frolov. Detergent-Assisted Protein Digestion—On the Way to Avoid the Key Bottleneck of Shotgun Bottom-Up Proteomics. International Journal of Molecular Sciences 2022, 23 (22) , 13903.
    64. Lauren B. Arendse, James M. Murithi, Tarrick Qahash, Charisse Flerida A. Pasaje, Luiz C. Godoy, Sumanta Dey, Liezl Gibhard, Sonja Ghidelli-Disse, Gerard Drewes, Marcus Bantscheff, Maria J. Lafuente-Monasterio, Stephen Fienberg, Lynn Wambua, Samuel Gachuhi, Dina Coertzen, Mariëtte van der Watt, Janette Reader, Ayesha S. Aswat, Erica Erlank, Nelius Venter, Nimisha Mittal, Madeline R. Luth, Sabine Ottilie, Elizabeth A. Winzeler, Lizette L. Koekemoer, Lyn-Marie Birkholtz, Jacquin C. Niles, Manuel Llinás, David A. Fidock, Kelly Chibale. The anticancer human mTOR inhibitor sapanisertib potently inhibits multiple Plasmodium kinases and life cycle stages. Science Translational Medicine 2022, 14 (667)
    65. Isabel M. Diaz Lozano, Helena Sork, Virginia M. Stone, Maria Eldh, Xiaofang Cao, Maria Pernemalm, Susanne Gabrielsson, Malin Flodström-Tullberg. Proteome profiling of whole plasma and plasma-derived extracellular vesicles facilitates the detection of tissue biomarkers in the non-obese diabetic mouse. Frontiers in Endocrinology 2022, 13
    66. Jonas Weidenhausen, Jürgen Kopp, Carmen Ruger-Herreros, Frank Stein, Per Haberkant, Karine Lapouge, Irmgard Sinning. Extended N-Terminal Acetyltransferase Naa50 in Filamentous Fungi Adds to Naa50 Diversity. International Journal of Molecular Sciences 2022, 23 (18) , 10805.
    67. María Trelis, Christian M. Sánchez-López, Liz F. Sánchez-Palencia, Victor Ramírez-Toledo, Antonio Marcilla, Dolores Bernal. Proteomic Analysis of Extracellular Vesicles From Fasciola hepatica Hatching Eggs and Juveniles in Culture. Frontiers in Cellular and Infection Microbiology 2022, 12
    68. Gonçalo Garcia, Adelaide Fernandes, Frank Stein, Dora Brites. Protective Signature of IFNγ-Stimulated Microglia Relies on miR-124-3p Regulation From the Secretome Released by Mutant APP Swedish Neuronal Cells. Frontiers in Pharmacology 2022, 13
    69. Marion Flipo, Rosangela Frita, Marilyne Bourotte, María S. Martínez-Martínez, Markus Boesche, Gary W. Boyle, Geo Derimanov, Gerard Drewes, Pablo Gamallo, Sonja Ghidelli-Disse, Stephanie Gresham, Elena Jiménez, Jaime de Mercado, Esther Pérez-Herrán, Esther Porras-De Francisco, Joaquín Rullas, Patricia Casado, Florence Leroux, Catherine Piveteau, Mehdi Kiass, Vanessa Mathys, Karine Soetaert, Véronique Megalizzi, Abdalkarim Tanina, René Wintjens, Rudy Antoine, Priscille Brodin, Vincent Delorme, Martin Moune, Kamel Djaout, Stéphanie Slupek, Christian Kemmer, Marc Gitzinger, Lluis Ballell, Alfonso Mendoza-Losana, Sergio Lociuro, Benoit Deprez, David Barros-Aguirre, Modesto J. Remuiñán, Nicolas Willand, Alain R. Baulard. The small-molecule SMARt751 reverses Mycobacterium tuberculosis resistance to ethionamide in acute and chronic mouse models of tuberculosis. Science Translational Medicine 2022, 14 (643)
    70. Gülkiz Baytek, Oliver Popp, Philipp Mertins, Baris Tursun. Robust co-immunoprecipitation with mass spectrometry for Caenorhabditis elegans using solid-phase enhanced sample preparation. BioTechniques 2022, 72 (5) , 175-184.
    71. Urszula Rykaczewska, Quanyi Zhao, Peter Saliba-Gustafsson, Mariette Lengquist, Malin Kronqvist, Otto Bergman, Zhiqiang Huang, Kent Lund, Katarina Waden, Vila Z. Pons, Kenneth Caidahl, Josefin Skogsberg, Vladana Vukojevic, Jan H.N. Lindeman, Joy Roy, Göran K. Hansson, Eckardt Treuter, Nicholas J. Leeper, Per Eriksson, Ewa Ehrenborg, Anton Razuvaev, Ulf Hedin, Ljubica Matic. Plaque Evaluation by Ultrasound and Transcriptomics Reveals BCLAF1 as a Regulator of Smooth Muscle Cell Lipid Transdifferentiation in Atherosclerosis. Arteriosclerosis, Thrombosis, and Vascular Biology 2022,
    72. Angela R. S. Kruse, Jeffrey M. Spraggins. Uncovering Molecular Heterogeneity in the Kidney With Spatially Targeted Mass Spectrometry. Frontiers in Physiology 2022, 13
    73. Federica Anastasi, Marialaura Dilillo, Davide Pellegrini, Liam A. McDonnell. Isolation and Proteomic Analysis of Mouse Serum Small Extracellular Vesicles for Individual Subject Analysis. 2022, 41-54.
    74. Conrad T. Pfeiffer, Joao A. Paulo, Steven P. Gygi, Howard A. Rockman. Proximity labeling for investigating protein-protein interactions. 2022, 237-266.
    75. Sylvain Lefort, Amal El-Naggar, Susanna Tan, Shane Colborne, Gian Luca Negri, Davide Pellacani, Martin Hirst, Barry Gusterson, Gregg B. Morin, Poul H. Sorensen, Connie J. Eaves. De novo and cell line models of human mammary cell transformation reveal an essential role for Yb-1 in multiple stages of human breast cancer. Cell Death & Differentiation 2022, 29 (1) , 54-64.
    76. Sophia Rossouw, Hocine Bendou, Liam Bell, Jonathan Rigby, Alan Christoffels. Effect of polyethylene glycol 20 000 on protein extraction efficiency of formalin-fixed paraffin-embedded tissues in South Africa. African Journal of Laboratory Medicine 2021, 10 (1)
    77. Amanda Khoo, Lydia Y. Liu, Julius O. Nyalwidhe, O. John Semmes, Danny Vesprini, Michelle R. Downes, Paul C. Boutros, Stanley K. Liu, Thomas Kislinger. Proteomic discovery of non-invasive biomarkers of localized prostate cancer using mass spectrometry. Nature Reviews Urology 2021, 18 (12) , 707-724.
    78. Alice R. Moorey, Alejandro Cabanillas, Sarah M. Batt, Sonja Ghidelli-Disse, Beatriz Urones, Olalla Sanz, Joel Lelievre, Marcus Bantscheff, Liam R. Cox, Gurdyal S. Besra. The multi-target aspect of an MmpL3 inhibitor: The BM212 series of compounds bind EthR2, a transcriptional regulator of ethionamide activation. The Cell Surface 2021, 7 , 100068.
    79. Chun-Ying Wang, Martin Lempp, Niklas Farke, Stefano Donati, Timo Glatter, Hannes Link. Metabolome and proteome analyses reveal transcriptional misregulation in glycolysis of engineered E. coli. Nature Communications 2021, 12 (1)
    80. Luis Daniel Cruz-Zaragoza, Sven Dennerlein, Andreas Linden, Roya Yousefi, Elena Lavdovskaia, Abhishek Aich, Rebecca R. Falk, Ridhima Gomkale, Thomas Schöndorf, Markus T. Bohnsack, Ricarda Richter-Dennerlein, Henning Urlaub, Peter Rehling. An in vitro system to silence mitochondrial gene expression. Cell 2021, 184 (23) , 5824-5837.e15.
    81. Hao Cheng, Hangrui Liu, Weihua Li, Ming Li. Recent advances in magnetic digital microfluidic platforms. ELECTROPHORESIS 2021, 42 (21-22) , 2329-2346.
    82. Xinyue Liu, Rose Fields, Devin K. Schweppe, Joao A. Paulo. Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging. Expert Review of Proteomics 2021, 18 (9) , 795-807.
    83. Sophie A. Herbst, Marta Stolarczyk, Tina Becirovic, Felix Czernilofsky, Yi Liu, Carolin Kolb, Mareike Knoll, Marco Herling, Carsten Müller-Tidow, Sascha Dietrich. Phagocytosis by stroma confounds coculture studies. iScience 2021, 24 (9) , 103062.
    84. Anna M Schlagowski, Katharina Knöringer, Sandrine Morlot, Ana Sánchez Vicente, Tamara Flohr, Lena Krämer, Felix Boos, Nabeel Khalid, Sheraz Ahmed, Jana Schramm, Lena M Murschall, Per Haberkant, Frank Stein, Jan Riemer, Benedikt Westermann, Ralf J Braun, Konstanze F Winklhofer, Gilles Charvin, Johannes M Herrmann. Increased levels of mitochondrial import factor Mia40 prevent the aggregation of polyQ proteins in the cytosol. The EMBO Journal 2021, 40 (16)
    85. Dimitris C. Kanellis, Jaime A. Espinoza, Asimina Zisi, Elpidoforos Sakkas, Jirina Bartkova, Anna-Maria Katsori, Johan Boström, Lars Dyrskjøt, Helle Broholm, Mikael Altun, Simon J. Elsässer, Mikael S. Lindström, Jiri Bartek. The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output. Science Advances 2021, 7 (32)
    86. Yuanyue Li, Michael Kuhn, Joanna Zukowska-Kasprzyk, Marco L. Hennrich, Panagiotis L. Kastritis, Francis J. O’Reilly, Prasad Phapale, Martin Beck, Anne-Claude Gavin, Peer Bork, . Coupling proteomics and metabolomics for the unsupervised identification of protein–metabolite interactions in Chaetomium thermophilum. PLOS ONE 2021, 16 (7) , e0254429.
    87. Kidon Sung, Jungwhan Chon, Ohgew Kweon, Seongwon Nho, Seongjae Kim, Miseon Park, Angel Paredes, Jin-Hee Lim, Saeed A. Khan, Kenneth Scott Phillips, Carl E. Cerniglia. Dynamic Adaptive Response of Pseudomonas aeruginosa to Clindamycin/Rifampicin-Impregnated Catheters. Antibiotics 2021, 10 (7) , 752.
    88. Rosanne E. Veerman, Loes Teeuwen, Paulo Czarnewski, Gözde Güclüler Akpinar, AnnSofi Sandberg, Xiaofang Cao, Maria Pernemalm, Lukas M. Orre, Susanne Gabrielsson, Maria Eldh. Molecular evaluation of five different isolation methods for extracellular vesicles reveals different clinical applicability and subcellular origin. Journal of Extracellular Vesicles 2021, 10 (9)
    89. Natalia Mast, Alexey M. Petrov, Erin Prendergast, Ilya Bederman, Irina A. Pikuleva. Brain Acetyl-CoA Production and Phosphorylation of Cytoskeletal Proteins Are Targets of CYP46A1 Activity Modulation and Altered Sterol Flux. Neurotherapeutics 2021, 18 (3) , 2040-2060.
    90. Yiheng Mao, Xi Wang, Peiwu Huang, Ruijun Tian. Spatial proteomics for understanding the tissue microenvironment. The Analyst 2021, 146 (12) , 3777-3798.
    91. Kanoknate Supasri, Manoj Kumar, Mano Mathew, Bethany Signal, Matthew Padula, David Suggett, Peter Ralph. Evaluation of Filter, Paramagnetic, and STAGETips Aided Workflows for Proteome Profiling of Symbiodiniaceae Dinoflagellate. Processes 2021, 9 (6) , 983.
    92. Tianyang Yan, Heta S. Desai, Lisa M. Boatner, Stephanie L. Yen, Jian Cao, Maria F. Palafox, Yasaman Jami‐Alahmadi, Keriann M. Backus. SP3‐FAIMS Chemoproteomics for High‐Coverage Profiling of the Human Cysteinome**. ChemBioChem 2021, 22 (10) , 1841-1851.
    93. Sophia C. Rossouw, Hocine Bendou, Renette J. Blignaut, Liam Bell, Jonathan Rigby, Alan Christoffels. Evaluation of Protein Purification Techniques and Effects of Storage Duration on LC-MS/MS Analysis of Archived FFPE Human CRC Tissues. Pathology and Oncology Research 2021, 27
    94. Glendon J. Parker, Heather E. McKiernan, Kevin M. Legg, Zachary C. Goecker. Forensic Proteomics. Forensic Science International: Genetics 2021, 2009 , 102529.
    95. Tian Mou, Yudi Pawitan, Matthias Stahl, Mattias Vesterlund, Wenjiang Deng, Rozbeh Jafari, Anna Bohlin, Albin Österroos, Loannis Siavelis, Helena Bäckvall, Tom Erkers, Santeri Kiviluoto, Brinton Seashore‐Ludlow, Päivi Östling, Lukas M. Orre, Olli Kallioniemi, Sören Lehmann, Janne Lehtiö, Trung Nghia Vu. The transcriptome‐wide landscape of molecular subtype‐specific mRNA expression profiles in acute myeloid leukemia. American Journal of Hematology 2021, 96 (5) , 580-588.
    96. Joao A. Paulo, Devin K. Schweppe. Advances in quantitative high‐throughput phosphoproteomics with sample multiplexing. PROTEOMICS 2021, 21 (9)
    97. Marta Barbosa, Cátia Gomes, Catarina Sequeira, Joana Gonçalves-Ribeiro, Carolina Campos Pina, Luís A. Carvalho, Rui Moreira, Sandra H. Vaz, Ana Rita Vaz, Dora Brites. Recovery of Depleted miR-146a in ALS Cortical Astrocytes Reverts Cell Aberrancies and Prevents Paracrine Pathogenicity on Microglia and Motor Neurons. Frontiers in Cell and Developmental Biology 2021, 9
    98. Aurélia C. Balestra, Konstantinos Koussis, Natacha Klages, Steven A. Howell, Helen R. Flynn, Marcus Bantscheff, Carla Pasquarello, Abigail J. Perrin, Lorenzo Brusini, Patrizia Arboit, Olalla Sanz, Laura Peces-Barba Castaño, Chrislaine Withers-Martinez, Alexandre Hainard, Sonja Ghidelli-Disse, Ambrosius P. Snijders, David A. Baker, Michael J. Blackman, Mathieu Brochet. Ca 2+ signals critical for egress and gametogenesis in malaria parasites depend on a multipass membrane protein that interacts with PKG. Science Advances 2021, 7 (13)
    99. Yu Gao, Ruining Liu, Chenfei He, Juan Basile, Mattias Vesterlund, Marie Wahren-Herlenius, Alexander Espinoza, Cassandra Hokka-Zakrisson, Fahad Zadjali, Akihiko Yoshimura, Mikael Karlsson, Berit Carow, Martin E. Rottenberg. SOCS3 Expression by Thymic Stromal Cells Is Required for Normal T Cell Development. Frontiers in Immunology 2021, 12
    100. Kamil Mikulášek, Hana Konečná, David Potěšil, Renata Holánková, Jan Havliš, Zbyněk Zdráhal. SP3 Protocol for Proteomic Plant Sample Preparation Prior LC-MS/MS. Frontiers in Plant Science 2021, 12
    Load all citations

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    Pair your accounts.

    Export articles to Mendeley

    Get article recommendations from ACS based on references in your Mendeley library.

    You’ve supercharged your research process with ACS and Mendeley!

    STEP 1:
    Click to create an ACS ID

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

    Your Mendeley pairing has expired. Please reconnect