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

Consecutive Proteolytic Digestion in an Enzyme Reactor Increases Depth of Proteomic and Phosphoproteomic Analysis

View Author Information
Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany
Cite this: Anal. Chem. 2012, 84, 6, 2631–2637
Publication Date (Web):February 12, 2012
Copyright © 2012 American Chemical Society

    Article Views





    Other access options
    Supporting Info (6)»


    Abstract Image

    Analytical advantages of using multiple enzymes for sample digestion (MED), primarily an increase of sequence coverage, have been reported in several studies. However, this approach is only rarely used, mainly because it requires additional sample and mass spectrometric measurement time. We have previously described Filter Aided Sample Preparation (FASP), a type of proteomic reactor, in which samples dissolved in sodium dodecyl sulfate (SDS) are digested in an ultrafiltration unit. In FASP, such as in any other preparation protocol, a portion of sample remains after digestion and peptide elution. Making use of this fact, we here develop a protocol enabling consecutive digestion of the sample with two or three enzymes. By use of the FASP method, peptides are liberated after each digestion step and remaining material is subsequently cleaved with the next proteinase. We observed excellent performance of the ultrafiltration devices in this mode, allowing efficient separation of orthogonal populations of peptides, resulting in an increase in the numbers of identified peptides and proteins. At the low microgram level, we found that the consecutive use of endoproteinases LysC and trypsin enabled identification of up to 40% more proteins and phosphorylation sites in comparison to the commonly used one-step tryptic digestion. MED-FASP offers efficient exploration of previously unused sample material, increasing depth of proteomic analyses and sequence coverage.

    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

    Six tables as described in the text (xls). This material is available free of charge via the Internet at

    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 255 publications.

    1. Matthew D. Harwood, Katharina Zettl, Manuel Weinheimer, Venkatesh Pilla-Reddy, Hong Shen, Frank Jacobs, Xiaoyan Chu, Felix Huth, Masanori Nakakariya, Paresh P. Chothe, Sibylle Neuhoff, Jacek R. Wiśniewski. Interlaboratory Variability in the Madin–Darby Canine Kidney Cell Proteome. Molecular Pharmaceutics 2023, 20 (7) , 3505-3518.
    2. Christine Wegler, Pär Matsson, Veronica Krogstad, Jozef Urdzik, Hege Christensen, Tommy B. Andersson, Per Artursson. Influence of Proteome Profiles and Intracellular Drug Exposure on Differences in CYP Activity in Donor-Matched Human Liver Microsomes and Hepatocytes. Molecular Pharmaceutics 2021, 18 (4) , 1792-1805.
    3. Therese Dau, Giulia Bartolomucci, Juri Rappsilber. Proteomics Using Protease Alternatives to Trypsin Benefits from Sequential Digestion with Trypsin. Analytical Chemistry 2020, 92 (14) , 9523-9527.
    4. 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.
    5. Denis Morsa, Dominique Baiwir, Raphaël La Rocca, Tyler A. Zimmerman, Emeline Hanozin, Elodie Grifnée, Rémi Longuespée, Marie-Alice Meuwis, Nicolas Smargiasso, Edwin De Pauw, Gabriel Mazzucchelli. Multi-Enzymatic Limited Digestion: The Next-Generation Sequencing for Proteomics?. Journal of Proteome Research 2019, 18 (6) , 2501-2513.
    6. Yi-Han Lin, Rodrigo Vargas Eguez, Manolito G. Torralba, Harinder Singh, Pawel Golusinski, Wojciech Golusinski, Michal Masternak, Karen E. Nelson, Marcelo Freire, Yanbao Yu. Self-Assembled STrap for Global Proteomics and Salivary Biomarker Discovery. Journal of Proteome Research 2019, 18 (4) , 1907-1915.
    7. Therese Dau, Kapil Gupta, Imre Berger, Juri Rappsilber. Sequential Digestion with Trypsin and Elastase in Cross-Linking Mass Spectrometry. Analytical Chemistry 2019, 91 (7) , 4472-4478.
    8. Jacek R Wiśniewski, Christine Wegler, Per Artursson. Multiple-Enzyme-Digestion Strategy Improves Accuracy and Sensitivity of Label- and Standard-Free Absolute Quantification to a Level That Is Achievable by Analysis with Stable Isotope-Labeled Standard Spiking. Journal of Proteome Research 2019, 18 (1) , 217-224.
    9. Milkessa HaileMariam, Rodrigo Vargas Eguez, Harinder Singh, Shiferaw Bekele, Gobena Ameni, Rembert Pieper, Yanbao Yu. S-Trap, an Ultrafast Sample-Preparation Approach for Shotgun Proteomics. Journal of Proteome Research 2018, 17 (9) , 2917-2924.
    10. Zhen Wu, Jichang Huang, Jingnan Huang, Qingqing Li, Xumin Zhang. Lys-C/Arg-C, a More Specific and Efficient Digestion Approach for Proteomics Studies. Analytical Chemistry 2018, 90 (16) , 9700-9707.
    11. Lazaro Hiram Betancourt, Aniel Sanchez, Indira Pla, Magdalena Kuras, Qimin Zhou, Roland Andersson, Gyorgy Marko-Varga. Quantitative Assessment of Urea In-Solution Lys-C/Trypsin Digestions Reveals Superior Performance at Room Temperature over Traditional Proteolysis at 37 °C. Journal of Proteome Research 2018, 17 (7) , 2556-2561.
    12. Andrea Treyer, André Mateus, Jacek R Wiśniewski, Hinnerk Boriss, Pär Matsson, Per Artursson. Intracellular Drug Bioavailability: Effect of Neutral Lipids and Phospholipids. Molecular Pharmaceutics 2018, 15 (6) , 2224-2233.
    13. Zhen Wu, Jichang Huang, Jianan Lu, and Xumin Zhang . Reversible Lysine Derivatization Enabling Improved Arg-C Digestion, a Highly Specific Arg-C Digestion Using Trypsin. Analytical Chemistry 2018, 90 (3) , 1554-1559.
    14. Liangliang Ren, Chaoying Li, Wenli Shao, Weiran Lin, Fuchu He, and Ying Jiang . TiO2 with Tandem Fractionation (TAFT): An Approach for Rapid, Deep, Reproducible, and High-Throughput Phosphoproteome Analysis. Journal of Proteome Research 2018, 17 (1) , 710-721.
    15. Veronika Kuchařová Pettersen, Hans Steinsland, and Harald G. Wiker . Comparative Proteomics of Enterotoxigenic Escherichia coli Reveals Differences in Surface Protein Production and Similarities in Metabolism. Journal of Proteome Research 2018, 17 (1) , 325-336.
    16. Malte Sielaff, Jörg Kuharev, Toszka Bohn, Jennifer Hahlbrock, Tobias Bopp, Stefan Tenzer, and Ute Distler . Evaluation of FASP, SP3, and iST Protocols for Proteomic Sample Preparation in the Low Microgram Range. Journal of Proteome Research 2017, 16 (11) , 4060-4072.
    17. Irena Dapic, Naomi Uwugiaren, Petra J. Jansen, and Garry L. Corthals . Fast and Simple Protocols for Mass Spectrometry-Based Proteomics of Small Fresh Frozen Uterine Tissue Sections. Analytical Chemistry 2017, 89 (20) , 10769-10775.
    18. Christine Wegler, Fabienne Z. Gaugaz, Tommy B. Andersson, Jacek R. Wiśniewski, Diana Busch, Christian Gröer, Stefan Oswald, Agneta Norén, Frederik Weiss, Helen S. Hammer, Thomas O. Joos, Oliver Poetz, Brahim Achour, Amin Rostami-Hodjegan, Evita van de Steeg, Heleen M. Wortelboer, and Per Artursson . Variability in Mass Spectrometry-based Quantification of Clinically Relevant Drug Transporters and Drug Metabolizing Enzymes. Molecular Pharmaceutics 2017, 14 (9) , 3142-3151.
    19. Agata H. Bryk and Jacek R. Wiśniewski . Quantitative Analysis of Human Red Blood Cell Proteome. Journal of Proteome Research 2017, 16 (8) , 2752-2761.
    20. Aaron Millan-Oropeza, Céline Henry, Mélisande Blein-Nicolas, Anne Aubert-Frambourg, Fathi Moussa, Jean Bleton, and Marie-Jöelle Virolle . Quantitative Proteomics Analysis Confirmed Oxidative Metabolism Predominates in Streptomyces coelicolor versus Glycolytic Metabolism in Streptomyces lividans. Journal of Proteome Research 2017, 16 (7) , 2597-2613.
    21. Simon Davis, Philip D. Charles, Lin He, Peter Mowlds, Benedikt M. Kessler, and Roman Fischer . Expanding Proteome Coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) Combined with Broad Specificity Proteolysis. Journal of Proteome Research 2017, 16 (3) , 1288-1299.
    22. Dariusz Rakus, Agnieszka Gizak, and Jacek R. Wiśniewski . Proteomics Unveils Fibroblast–Cardiomyocyte Lactate Shuttle and Hexokinase Paradox in Mouse Muscles. Journal of Proteome Research 2016, 15 (8) , 2479-2490.
    23. Jacek R. Wiśniewski and Matthias Mann . A Proteomics Approach to the Protein Normalization Problem: Selection of Unvarying Proteins for MS-Based Proteomics and Western Blotting. Journal of Proteome Research 2016, 15 (7) , 2321-2326.
    24. Jacek R. Wiśniewski . Quantitative Evaluation of Filter Aided Sample Preparation (FASP) and Multienzyme Digestion FASP Protocols. Analytical Chemistry 2016, 88 (10) , 5438-5443.
    25. Walid S. Maaty and David D. Weis . Label-Free, In-Solution Screening of Peptide Libraries for Binding to Protein Targets Using Hydrogen Exchange Mass Spectrometry. Journal of the American Chemical Society 2016, 138 (4) , 1335-1343.
    26. Nicholas M. Riley and Joshua J. Coon . Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling. Analytical Chemistry 2016, 88 (1) , 74-94.
    27. Janice Mayne, Zhibin Ning, Xu Zhang, Amanda E. Starr, Rui Chen, Shelley Deeke, Cheng-Kang Chiang, Bo Xu, Ming Wen, Kai Cheng, Deeptee Seebun, Alexandra Star, Jasmine I. Moore, and Daniel Figeys . Bottom-Up Proteomics (2013–2015): Keeping up in the Era of Systems Biology. Analytical Chemistry 2016, 88 (1) , 95-121.
    28. Wai-Kok Choong, Hui-Yin Chang, Ching-Tai Chen, Chia-Feng Tsai, Wen-Lian Hsu, Yu-Ju Chen, and Ting-Yi Sung . Informatics View on the Challenges of Identifying Missing Proteins from Shotgun Proteomics. Journal of Proteome Research 2015, 14 (12) , 5396-5407.
    29. Timo Glatter, Erik Ahrné, and Alexander Schmidt . Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells. Journal of Proteome Research 2015, 14 (11) , 4472-4485.
    30. Jacek R. Wiśniewski, Kamila Duś-Szachniewicz, Paweł Ostasiewicz, Piotr Ziółkowski, Dariusz Rakus, and Matthias Mann . Absolute Proteome Analysis of Colorectal Mucosa, Adenoma, and Cancer Reveals Drastic Changes in Fatty Acid Metabolism and Plasma Membrane Transporters. Journal of Proteome Research 2015, 14 (9) , 4005-4018.
    31. Jacek R. Wiśniewski, Agnieszka Gizak, and Dariusz Rakus . Integrating Proteomics and Enzyme Kinetics Reveals Tissue-Specific Types of the Glycolytic and Gluconeogenic Pathways. Journal of Proteome Research 2015, 14 (8) , 3263-3273.
    32. Richard J. Giannone, Louie L. Wurch, Mircea Podar, and Robert L. Hettich . Rescuing Those Left Behind: Recovering and Characterizing Underdigested Membrane and Hydrophobic Proteins To Enhance Proteome Measurement Depth. Analytical Chemistry 2015, 87 (15) , 7720-7728.
    33. Jacek R. Wiśniewski and Gabriela Pruś . Homogenous Phase Enrichment of Cysteine-Containing Peptides for Improved Proteome Coverage. Analytical Chemistry 2015, 87 (13) , 6861-6867.
    34. Sylvester M. Greer, W. Ryan Parker, and Jennifer S. Brodbelt . Impact of Protease on Ultraviolet Photodissociation Mass Spectrometry for Bottom-up Proteomics. Journal of Proteome Research 2015, 14 (6) , 2626-2632.
    35. Dariusz Rakus, Agnieszka Gizak, Atul Deshmukh, and Jacek R. Wiśniewski . Absolute Quantitative Profiling of the Key Metabolic Pathways in Slow and Fast Skeletal Muscle. Journal of Proteome Research 2015, 14 (3) , 1400-1411.
    36. Nadine A. Binai, Fabio Marino, Peter Soendergaard, Nicolai Bache, Shabaz Mohammed, and Albert J. R. Heck . Rapid Analyses of Proteomes and Interactomes Using an Integrated Solid-Phase Extraction–Liquid Chromatography–MS/MS System. Journal of Proteome Research 2015, 14 (2) , 977-985.
    37. Jacek R. Wiśniewski, Alexandra Friedrich, Thorsten Keller, Matthias Mann, and Hermann Koepsell . The Impact of High-Fat Diet on Metabolism and Immune Defense in Small Intestine Mucosa. Journal of Proteome Research 2015, 14 (1) , 353-365.
    38. Jonathan Erde, Rachel R. Ogorzalek Loo, and Joseph A. Loo . Enhanced FASP (eFASP) to Increase Proteome Coverage and Sample Recovery for Quantitative Proteomic Experiments. Journal of Proteome Research 2014, 13 (4) , 1885-1895.
    39. Chao Fan, Zhaomei Shi, Yiting Pan, Zifeng Song, Wanjun Zhang, Xinyuan Zhao, Fang Tian, Bo Peng, Weijie Qin, Yun Cai, and Xiaohong Qian . Dual Matrix-Based Immobilized Trypsin for Complementary Proteolytic Digestion and Fast Proteomics Analysis with Higher Protein Sequence Coverage. Analytical Chemistry 2014, 86 (3) , 1452-1458.
    40. Janice Mayne, Amanda E. Starr, Zhibin Ning, Rui Chen, Cheng-Kang Chiang, and Daniel Figeys . Fine Tuning of Proteomic Technologies to Improve Biological Findings: Advancements in 2011–2013. Analytical Chemistry 2014, 86 (1) , 176-195.
    41. Scott J. Walmsley, Paul A. Rudnick, Yuxue Liang, Qian Dong, Stephen E. Stein, and Alexey I. Nesvizhskii . Comprehensive Analysis of Protein Digestion Using Six Trypsins Reveals the Origin of Trypsin As a Significant Source of Variability in Proteomics. Journal of Proteome Research 2013, 12 (12) , 5666-5680.
    42. Philip L. Loziuk, Jack Wang, Quanzi Li, Ronald R. Sederoff, Vincent L. Chiang, and David C. Muddiman . Understanding the Role of Proteolytic Digestion on Discovery and Targeted Proteomic Measurements Using Liquid Chromatography Tandem Mass Spectrometry and Design of Experiments. Journal of Proteome Research 2013, 12 (12) , 5820-5829.
    43. Qun Zhao, Yu Liang, Huiming Yuan, Zhigang Sui, Qi Wu, Zhen Liang, Lihua Zhang, and Yukui Zhang . Biphasic Microreactor for Efficient Membrane Protein Pretreatment with a Combination of Formic Acid Assisted Solubilization, On-Column pH Adjustment, Reduction, Alkylation, and Tryptic Digestion. Analytical Chemistry 2013, 85 (18) , 8507-8512.
    44. Gary S. McDowell, Aleksandr Gaun, and Hanno Steen . iFASP: Combining Isobaric Mass Tagging with Filter-Aided Sample Preparation. Journal of Proteome Research 2013, 12 (8) , 3809-3812.
    45. Lancia N. F. Darville and Bernd H. A. Sokolowski . In-depth Proteomic Analysis of Mouse Cochlear Sensory Epithelium by Mass Spectrometry. Journal of Proteome Research 2013, 12 (8) , 3620-3630.
    46. Jordan T. Stobaugh, Kaitlin M. Fague, and James W. Jorgenson . Prefractionation of Intact Proteins by Reversed-Phase and Anion-Exchange Chromatography for the Differential Proteomic Analysis of Saccharomyces cerevisiae. Journal of Proteome Research 2013, 12 (2) , 626-636.
    47. Timo Glatter, Christina Ludwig, Erik Ahrné, Ruedi Aebersold, Albert J. R. Heck, and Alexander Schmidt . Large-Scale Quantitative Assessment of Different In-Solution Protein Digestion Protocols Reveals Superior Cleavage Efficiency of Tandem Lys-C/Trypsin Proteolysis over Trypsin Digestion. Journal of Proteome Research 2012, 11 (11) , 5145-5156.
    48. Sook Wah Yee, Luis Ferrández-Peral, Pol Alentorn-Moron, Claudia Fontsere, Merve Ceylan, Megan L. Koleske, Niklas Handin, Virginia M. Artegoitia, Giovanni Lara, Huan-Chieh Chien, Xujia Zhou, Jacques Dainat, Arthur Zalevsky, Andrej Sali, Colin M. Brand, Finn D. Wolfreys, Jia Yang, Jason E. Gestwicki, John A. Capra, Per Artursson, John W. Newman, Tomàs Marquès-Bonet, Kathleen M. Giacomini. Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates. Nature Communications 2024, 15 (1)
    49. Shevan Wilkin, Liam T. Lanigan, Nuria Montes, Mukul Sharma, Charlotte Avanzi, Donikë Sejdiu, Kerttu Majander, Saskia Pfrengle, Yun Chiang, Laura Kunz, Antje Dittmann, Frank Rühli, Pushpendra Singh, Maria Fontanals Coll, Matthew J. Collins, Alberto J. Taurozzi, Verena J. Schuenemann. Sequential trypsin and ProAlanase digestions unearth immunological protein biomarkers shrouded by skeletal collagen. iScience 2024, 27 (5) , 109663.
    50. M. Shahid Mansuri, Shveta Bathla, TuKiet T. Lam, Angus C. Nairn, Kenneth R. Williams. Optimal conditions for carrying out trypsin digestions on complex proteomes: From bulk samples to single cells. Journal of Proteomics 2024, 297 , 105109.
    51. Daniel T. Cervone, Roger Moreno‐Justicia, Júlia Prats Quesada, Atul S. Deshmukh. Mass spectrometry‐based proteomics approaches to interrogate skeletal muscle adaptations to exercise. Scandinavian Journal of Medicine & Science in Sports 2024, 34 (1)
    52. Tejaswini Hipparagi, Shivaleela Biradar, Srushti S.C., Babu R.L.. Proteomics. 2024, 99-119.
    53. Gianluca Degliesposti. Peptide-Based Mass Spectrometry for the Investigation of Protein Complexes. 2024, 31-40.
    54. Javier Marín-Prida, Arielis Rodríguez-Ulloa, Vladimir Besada, Alexey Llopiz-Arzuaga, Nathália Vieira Batista, Ignacio Hernández-González, Nancy Pavón-Fuentes, Érica Leandro Marciano Vieira, Viviana Falcón-Cama, Emilio F. Acosta, Gillian Martínez-Donato, Majel Cervantes-Llanos, Dai Lingfeng, Luis J. González, Julio Raúl Fernández-Massó, Gerardo Guillén-Nieto, Eduardo Pentón-Arias, Flávio Almeida Amaral, Mauro Martins Teixeira, Giselle Pentón-Rol. The effects of Phycocyanobilin on experimental arthritis involve the reduction in nociception and synovial neutrophil infiltration, inhibition of cytokine production, and modulation of the neuronal proteome. Frontiers in Immunology 2023, 14
    55. Markus Hovd, Ida Robertsen, Line Kristin Johnson, Veronica Krogstad, Christine Wegler, Kine Eide Kvitne, Marianne Kristiansen Kringen, Eva Skovlund, Cecilia Karlsson, Shalini Andersson, Per Artursson, Rune Sandbu, Jøran Hjelmesæth, Anders Åsberg, Rasmus Jansson-Löfmark, Hege Christensen. Neither Gastric Bypass Surgery Nor Diet-Induced Weight-Loss Affect OATP1B1 Activity as Measured by Rosuvastatin Oral Clearance. Clinical Pharmacokinetics 2023, 62 (5) , 725-735.
    56. Binwen Sun, Zheyi Liu, Jin Liu, Shan Zhao, Liming Wang, Fangjun Wang. The utility of proteases in proteomics, from sequence profiling to structure and function analysis. PROTEOMICS 2023, 23 (6)
    57. Van-An Duong, Hookeun Lee. Bottom-Up Proteomics: Advancements in Sample Preparation. International Journal of Molecular Sciences 2023, 24 (6) , 5350.
    58. Emma A Hall, Dhivya Kumar, Suzanna L Prosser, Patricia L Yeyati, Vicente Herranz-Pérez, Jose Manuel García-Verdugo, Lorraine Rose, Lisa McKie, Daniel O Dodd, Peter A Tennant, Roly Megaw, Laura C Murphy, Marisa F Ferreira, Graeme Grimes, Lucy Williams, Tooba Quidwai, Laurence Pelletier, Jeremy F Reiter, Pleasantine Mill. Centriolar satellites expedite mother centriole remodeling to promote ciliogenesis. eLife 2023, 12
    59. Han-Min Wang, Chan-Yuan Zhang, Kai-Cheng Peng, Ze-Xin Chen, Jun-Wei Su, Yu-Fa Li, Wen-Feng Li, Qing-Yun Gao, Shi-Ling Zhang, Yu-Qing Chen, Qing Zhou, Cong Xu, Chong-Rui Xu, Zhen Wang, Jian Su, Hong-Hong Yan, Xu-Chao Zhang, Hua-Jun Chen, Yi-Long Wu, Jin-Ji Yang. Using patient-derived organoids to predict locally advanced or metastatic lung cancer tumor response: A real-world study. Cell Reports Medicine 2023, 4 (2) , 100911.
    60. Yifan Xing, Wenjing Sun, Yuying Sun, Jialin Li, Jie Zhang, Ting Wu, Tingting Song, Yuncong Yao, Ji Tian. MPK6‐mediated HY5 phosphorylation regulates light‐induced anthocyanin accumulation in apple fruit. Plant Biotechnology Journal 2023, 21 (2) , 283-301.
    61. Panshak P. Dakup, Song Feng, Tujin Shi, Jon M. Jacobs, H. Steven Wiley, Wei-Jun Qian. Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways. Molecules 2023, 28 (3) , 1143.
    62. Sandra Murphy, Kay Ohlendieck. Protein Digestion for 2D-DIGE Analysis. 2023, 339-349.
    63. Peter Blattmann, Ruedi Aebersold. OMICS – Mass Spectrometry-Based Proteomics in Systems Biology Research. 2023, 372-384.
    64. Guido Domingo, Luca Chiodaroli, Simone Parola, Milena Marsoni, Marcella Bracale, Candida Vannini. Proteomic characterization of Shiitake (Lentinula edodes) post-harvest fruit bodies grown on hardwood logs and isolation of an antibacterial serine protease inhibitor. Fungal Biology 2023, 127 (1-2) , 881-890.
    65. 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.
    66. Dania Vázquez-Blomquist, Anette Hardy-Sosa, Saiyet C. Baez, Vladimir Besada, Sucel Palomares, Osmany Guirola, Yassel Ramos, Jacek R. Wiśniewski, Luis Javier González, Iraldo Bello-Rivero. Proteomics and Phospho-Proteomics Profiling of the Co-Formulation of Type I and II Interferons, HeberFERON, in the Glioblastoma-Derived Cell Line U-87 MG. Cells 2022, 11 (24) , 4068.
    67. Marie Courçon, Cédric Badiou, Mathilde Louwagie, Sibyle Etievant, Michel Jaquinod, Gérard Lina, Virginie Brun. Targeted Proteomics Analysis of Staphylococcal Superantigenic Toxins in Menstrual Fluid from Women with Menstrual Toxic Shock Syndrome (mTSS). Toxins 2022, 14 (12) , 886.
    68. Tatiana Leonova, Christian Ihling, Mohamad Saoud, Nadezhda Frolova, Robert Rennert, Ludger A. Wessjohann, Andrej Frolov. Does filter-aided sample preparation provide sufficient method linearity for quantitative plant shotgun proteomics?. Frontiers in Plant Science 2022, 13
    69. 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.
    70. Kine Eide Kvitne, Veronica Krogstad, Christine Wegler, Line Kristin Johnson, Marianne K. Kringen, Markus Herberg Hovd, Jens K. Hertel, Maria Heijer, Rune Sandbu, Eva Skovlund, Per Artursson, Cecilia Karlsson, Shalini Andersson, Tommy B. Andersson, Jøran Hjelmesæth, Anders Åsberg, Rasmus Jansson‐Löfmark, Hege Christensen, Ida Robertsen. Short‐ and long‐term effects of body weight, calorie restriction and gastric bypass on CYP1A2, CYP2C19 and CYP2C9 activity. British Journal of Clinical Pharmacology 2022, 88 (9) , 4121-4133.
    71. Magdalena Oroń, Marcin Grochowski, Akanksha Jaiswar, Justyna Legierska, Kamil Jastrzębski, Magdalena Nowak-Niezgoda, Małgorzata Kołos, Wojciech Kaźmierczak, Tomasz Olesiński, Małgorzata Lenarcik, Magdalena Cybulska, Michał Mikula, Alicja Żylicz, Marta Miączyńska, Katharina Zettl, Jacek R. Wiśniewski, Dawid Walerych. The molecular network of the proteasome machinery inhibition response is orchestrated by HSP70, revealing vulnerabilities in cancer cells. Cell Reports 2022, 40 (13) , 111428.
    72. Sophie Ayama-Canden, Rodolfo Tondo, Liliana Piñeros, Noëlle Ninane, Catherine Demazy, Marc Dieu, Antoine Fattaccioli, Tijani Tabarrant, Stéphane Lucas, Davide Bonifazi, Carine Michiels. IGDQ motogenic peptide gradient induces directional cell migration through integrin (αv)β3 activation in MDA-MB-231 metastatic breast cancer cells. Neoplasia 2022, 31 , 100816.
    73. Kine Eide Kvitne, Kristine Hole, Veronica Krogstad, Birgit Malene Wollmann, Christine Wegler, Line K. Johnson, Jens K. Hertel, Per Artursson, Cecilia Karlsson, Shalini Andersson, Tommy B. Andersson, Rune Sandbu, Jøran Hjelmesæth, Eva Skovlund, Hege Christensen, Rasmus Jansson-Löfmark, Anders Åsberg, Espen Molden, Ida Robertsen. Correlations between 4β-hydroxycholesterol and hepatic and intestinal CYP3A4: protein expression, microsomal ex vivo activity, and in vivo activity in patients with a wide body weight range. European Journal of Clinical Pharmacology 2022, 78 (8) , 1289-1299.
    74. Shilin Gong, Xiaolan Hu, Shengshuang Chen, Baoqing Sun, Jian‐Lin Wu, Na Li. Dual roles of drug or its metabolite−protein conjugate: Cutting‐edge strategy of drug discovery using shotgun proteomics. Medicinal Research Reviews 2022, 42 (4) , 1704-1734.
    75. Eugene C. Chen, Pär Matsson, Mina Azimi, Xujia Zhou, Niklas Handin, Sook Wah Yee, Per Artursson, Kathleen M. Giacomini. High Throughput Screening of a Prescription Drug Library for Inhibitors of Organic Cation Transporter 3, OCT3. Pharmaceutical Research 2022, 39 (7) , 1599-1613.
    76. Alexander A. Zanker, Patrick Stargardt, Sophie C. Kurzbach, Chiara Turrina, Juergen Mairhofer, Sebastian P. Schwaminger, Sonja Berensmeier. Direct capture and selective elution of a secreted polyglutamate‐tagged nanobody using bare magnetic nanoparticles. Biotechnology Journal 2022, 17 (5)
    77. Christine Wegler, Jacek R. Wiśniewski, Ida Robertsen, Hege Christensen, Jens Kristoffer Hertel, Jøran Hjelmesæth, Rasmus Jansson‐Löfmark, Anders Åsberg, Tommy B. Andersson, Per Artursson. Drug Disposition Protein Quantification in Matched Human Jejunum and Liver From Donors With Obesity. Clinical Pharmacology & Therapeutics 2022, 111 (5) , 1142-1154.
    78. Yassel Ramos, Alexis Almeida, Jenis Carpio, Arielis Rodríguez‐Ulloa, Yasser Perera, Luis J. González, Jacek R. Wiśniewski, Vladimir Besada. Gel electrophoresis/electroelution sorting fractionator combined with filter‐aided sample preparation for deep proteomic analysis. Journal of Separation Science 2022, 45 (10) , 1784-1796.
    79. Milena Álvarez-Viñas, Noelia González-Ballesteros, M. Dolores Torres, Lucía López-Hortas, Candida Vanini, Guido Domingo, M. Carmen Rodríguez-Argüelles, Herminia Domínguez. Efficient extraction of carrageenans from Chondrus crispus for the green synthesis of gold nanoparticles and formulation of printable hydrogels. International Journal of Biological Macromolecules 2022, 206 , 553-566.
    80. Mauro Rosales, Arielis Rodríguez-Ulloa, George V. Pérez, Vladimir Besada, Thalia Soto, Yassel Ramos, Luis J. González, Katharina Zettl, Jacek R. Wiśniewski, Ke Yang, Yasser Perera, Silvio E. Perea. CIGB-300-Regulated Proteome Reveals Common and Tailored Response Patterns of AML Cells to CK2 Inhibition. Frontiers in Molecular Biosciences 2022, 9
    81. Ben Stocks, Alba Gonzalez-Franquesa, Melissa L. Borg, Marie Björnholm, Lili Niu, Juleen R. Zierath, Atul S. Deshmukh. Integrated Liver and Plasma Proteomics in Obese Mice Reveals Complex Metabolic Regulation. Molecular & Cellular Proteomics 2022, 21 (3) , 100207.
    82. Laura Hellinen, Ali Koskela, Elina Vattulainen, Mikko Liukkonen, Christine Wegler, Andrea Treyer, Niklas Handin, Richard Svensson, Timo Myöhänen, Antti Poso, Kai Kaarniranta, Per Artursson, Arto Urtti. Inhibition of prolyl oligopeptidase: A promising pathway to prevent the progression of age-related macular degeneration. Biomedicine & Pharmacotherapy 2022, 146 , 112501.
    83. Aneta Stachowicz, Niveda Sundararaman, Vidya Venkatraman, Jennifer Van Eyk, Justyna Fert-Bober. pH/Acetonitrile-Gradient Reversed-Phase Fractionation of Enriched Hyper-Citrullinated Library in Combination with LC–MS/MS Analysis for Confident Identification of Citrullinated Peptides. 2022, 107-126.
    84. Anthony A. Iannetta, Leslie M. Hicks. Maximizing Depth of PTM Coverage: Generating Robust MS Datasets for Computational Prediction Modeling. 2022, 1-41.
    85. Beatriz Bueschbell, Ana Beatriz Caniceiro, Pedro M.S. Suzano, Miguel Machuqueiro, Nícia Rosário-Ferreira, Irina S. Moreira. Network biology and artificial intelligence drive the understanding of the multidrug resistance phenotype in cancer. Drug Resistance Updates 2022, 60 , 100811.
    86. Kine Eide Kvitne, Ida Robertsen, Eva Skovlund, Hege Christensen, Veronica Krogstad, Christine Wegler, Philip Carlo Angeles, Birgit Malene Wollmann, Kristine Hole, Line Kristin Johnson, Rune Sandbu, Per Artursson, Cecilia Karlsson, Shalini Andersson, Tommy B. Andersson, Jøran Hjelmesæth, Rasmus Jansson‐Löfmark, Anders Åsberg. Short‐ and long‐term effects of body weight loss following calorie restriction and gastric bypass on CYP3A‐activity – a non‐randomized three‐armed controlled trial. Clinical and Translational Science 2022, 15 (1) , 221-233.
    87. Johan Vessby, Jacek R. Wisniewski, Cecilia Lindskog, Niclas Eriksson, Katja Gabrysch, Katharina Zettl, Alkwin Wanders, Marie Carlson, Fredrik Rorsman, Mikael Åberg. AGPAT1 as a Novel Colonic Biomarker for Discriminating Between Ulcerative Colitis With and Without Primary Sclerosing Cholangitis. Clinical and Translational Gastroenterology 2022, 13 (5) , e00486.
    88. Qin Wei, Pei-Ru Fan, Xuan Sun, Yan-Ping Huang, Zhao-Sheng Liu. A Microfluidic Platform for Proteomics Based on Enzyme Reactor Monolith Incorporated with Mesoporous Molecular Sieve Sba-15. SSRN Electronic Journal 2022, 84
    89. A. S. Deshmukh, D. E. Steenberg, M. Hostrup, J. B. Birk, J. K. Larsen, A. Santos, R. Kjøbsted, J. R. Hingst, C. C. Schéele, M. Murgia, B. Kiens, E. A. Richter, M. Mann, J. F. P. Wojtaszewski. Deep muscle-proteomic analysis of freeze-dried human muscle biopsies reveals fiber type-specific adaptations to exercise training. Nature Communications 2021, 12 (1)
    90. Niklas Handin, Evgeniya Mickols, Magnus Ölander, Jakob Rudfeldt, Kristin Blom, Frida Nyberg, Wojciech Senkowski, Jozef Urdzik, Varun Maturi, Mårten Fryknäs, Per Artursson. Conditions for maintenance of hepatocyte differentiation and function in 3D cultures. iScience 2021, 24 (11) , 103235.
    91. Francisco T. T. Cavalcante, Antônio L. G. Cavalcante, Isamayra G. de Sousa, Francisco S. Neto, José C. S. dos Santos. Current Status and Future Perspectives of Supports and Protocols for Enzyme Immobilization. Catalysts 2021, 11 (10) , 1222.
    92. Floriane Pailleux, Pauline Maes, Michel Jaquinod, Justine Barthelon, Marion Darnaud, Claire Lacoste, Yves Vandenbrouck, Benoît Gilquin, Mathilde Louwagie, Anne-Marie Hesse, Alexandra Kraut, Jérôme Garin, Vincent Leroy, Jean-Pierre Zarski, Christophe Bruley, Yohann Couté, Didier Samuel, Philippe Ichai, Jamila Faivre, Virginie Brun. Mass Spectrometry-Based Proteomics Reveal Alcohol Dehydrogenase 1B as a Blood Biomarker Candidate to Monitor Acetaminophen-Induced Liver Injury. International Journal of Molecular Sciences 2021, 22 (20) , 11071.
    93. Magnus Ölander, Christine Wegler, Inken Flörkemeier, Andrea Treyer, Niklas Handin, Jenny M. Pedersen, Anna Vildhede, André Mateus, Edward L. LeCluyse, Jozef Urdzik, Per Artursson. Hepatocyte size fractionation allows dissection of human liver zonation. Journal of Cellular Physiology 2021, 236 (8) , 5885-5894.
    94. Dominika Drulis-Fajdasz, Kinga Gostomska-Pampuch, Przemysław Duda, Jacek Roman Wiśniewski, Dariusz Rakus. Quantitative Proteomics Reveals Significant Differences between Mouse Brain Formations in Expression of Proteins Involved in Neuronal Plasticity during Aging. Cells 2021, 10 (8) , 2021.
    95. Kamila Duś-Szachniewicz, Katarzyna Gdesz-Birula, Krzysztof Zduniak, Jacek R. Wiśniewski. Proteomic-Based Analysis of Hypoxia- and Physioxia-Responsive Proteins and Pathways in Diffuse Large B-Cell Lymphoma. Cells 2021, 10 (8) , 2025.
    96. Liuqun Zhao, Gang Fu, Yanyan Cui, Zixiang Xu, Tao Cai, Dawei Zhang. Compensating Complete Loss of Signal Recognition Particle During Co-translational Protein Targeting by the Translation Speed and Accuracy. Frontiers in Microbiology 2021, 12
    97. Mauro Rosales, George V. Pérez, Ailyn C. Ramón, Yiliam Cruz, Arielis Rodríguez-Ulloa, Vladimir Besada, Yassel Ramos, Dania Vázquez-Blomquist, Evelin Caballero, Daylen Aguilar, Luis J. González, Katharina Zettl, Jacek R. Wiśniewski, Ke Yang, Yasser Perera, Silvio E. Perea. Targeting of Protein Kinase CK2 in Acute Myeloid Leukemia Cells Using the Clinical-Grade Synthetic-Peptide CIGB-300. Biomedicines 2021, 9 (7) , 766.
    98. Jakub Faktor, David R. Goodlett, Irena Dapic. Trends in Sample Preparation for Proteome Analysis. 2021
    99. Kinga Gostomska-Pampuch, Dominika Drulis-Fajdasz, Agnieszka Gizak, Jacek R. Wiśniewski, Dariusz Rakus. Absolute Proteome Analysis of Hippocampus, Cortex and Cerebellum in Aged and Young Mice Reveals Changes in Energy Metabolism. International Journal of Molecular Sciences 2021, 22 (12) , 6188.
    100. Alba Gonzalez-Franquesa, Ben Stocks, Sabina Chubanava, Helle B. Hattel, Roger Moreno-Justicia, Lone Peijs, Jonas T. Treebak, Juleen R. Zierath, Atul S. Deshmukh. Mass-spectrometry-based proteomics reveals mitochondrial supercomplexome plasticity. Cell Reports 2021, 35 (8) , 109180.
    Load more 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