Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics Based on Acid Extraction

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855

Universal sample preparation method for proteome analysis

Wiśniewski, J. R., Zougman, A., Nagaraj, N., & Mann, M. (2009) · Nature Methods · doi:10.1038/nmeth.1322 · Cited by 8,352

Global quantification of mammalian gene expression control

Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · cited 1×

The human microbiome project

Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007) · Nature · doi:10.1038/nature06244 · Cited by 6,091

Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips

Rappsilber, J., Mann, M., & Ishihama, Y. (2007) · Nature Protocols · doi:10.1038/nprot.2007.261 · Cited by 4,641

Current understanding of the human microbiome

Gilbert, J. A., Blaser, M. J., Caporaso, J. G., Jansson, J. K., Lynch, S. V., & Knight, R. (2018) · Nature Medicine · doi:10.1038/nm.4517 · Cited by 2,609

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

Kong, A. T., Leprevost, F. D. V., Avtonomov, D. M., Mellacheruvu, D., & Nesvizhskii, A. I. (2017) · Nature Methods · doi:10.1038/nmeth.4256 · Cited by 2,406

Mass-spectrometric exploration of proteome structure and function

Aebersold, R., & Mann, M. (2016) · Nature · doi:10.1038/nature19949 · Cited by 2,334

Direct analysis of protein complexes using mass spectrometry

Link, A. J., Eng, J. K., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., & Yates, J. R. (1999) · Nature Biotechnology · doi:10.1038/10890 · Cited by 2,218

Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

Kulak, N. A., Pichler, G., Paron, I., Nagaraj, N., & Mann, M. (2014) · Nature Methods · doi:10.1038/nmeth.2834 · Cited by 1,719

A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field

Dupree, E. J., Jayathirtha, M., Yorkey, H., Mihăşan, M., Petre, B. A., & Darie, C. C. (2020) · Proteomes · doi:10.3390/proteomes8030014 · Cited by 390

Bottom-Up Proteomics: Advancements in Sample Preparation

Duong, V., & Lee, H. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24065350 · Cited by 150

Omics-Driven Biotechnology for Industrial Applications

Amer, B., & Baidoo, E. E. K. (2021) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2021.613307 · Cited by 150

Solvent Precipitation SP3 (SP4) Enhances Recovery for Proteomics Sample Preparation without Magnetic Beads

Johnston, H. E., Yadav, K., Kirkpatrick, J. M., Biggs, G. S., Oxley, D., Kramer, H., & Samant, R. S. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.1c04200 · Cited by 136

In Search of a Universal Method: A Comparative Survey of Bottom-Up Proteomics Sample Preparation Methods

Varnavides, G., Madern, M., Anrather, D., Hartl, N., Reiter, W., & Hartl, M. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00265 · Cited by 122

Evaluation and Refinement of Sample Preparation Methods for Extracellular Matrix Proteome Coverage

McCabe, M. C., Schmitt, L. R., Hill, R. C., Dzieciątkowska, M., Maslanka, M. D., Daamen, W. F., Kuppevelt, T. H. V., Hof, D. J., & Hansen, K. C. (2021) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2021.100079 · Cited by 64

Universal Solid-Phase Protein Preparation (USP3) for Bottom-up and Top-down Proteomics

Dagley, L. F., Infusini, G., Larsen, R. H., Sandow, J. J., & Webb, A. I. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00217 · Cited by 71

Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves

Wu, C., Mori, M., Abele, M., Banaei‐Esfahani, A., Zhang, Z., Okano, H., Aebersold, R. H., Ludwig, C., & Hwa, T. (2023) · Nature Microbiology · doi:10.1038/s41564-022-01310-w · Cited by 52

Macrophage autophagy deficiency-induced CEBPB accumulation alleviates atopic dermatitis via impairing M2 polarization

Zhu, Y., Liu, Y., Ma, Y., Chen, L., Huang, H., Huang, S., Zhang, H., He, Y., Tan, C., He, Y., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113430 · Cited by 47

Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in Silico Peptide Mass Libraries

Lasch, P., Schneider, A., Blumenscheit, C., & Doellinger, J. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir120.002061 · Cited by 44

Perspective on Proteomics for Virus Detection in Clinical Samples

Grossegesse, M., Hartkopf, F., Nitsche, A., Schaade, L., Doellinger, J., & Muth, T. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00674 · Cited by 43

Amino acid availability acts as a metabolic rheostat to determine the magnitude of ILC2 responses

Hodge, S. H., Krauss, M. Z., Kaymak, I., King, J. I., Howden, A. J. M., Panić, G., Grencis, R. K., Swann, J. R., Sinclair, L. V., & Hepworth, M. R. (2022) · The Journal of Experimental Medicine · doi:10.1084/jem.20221073 · Cited by 42

Mass Spectrometric Analysis of Urine from COVID-19 Patients for Detection of SARS-CoV-2 Viral Antigen and to Study Host Response

Chavan, S., Mangalaparthi, K. K., Singh, S., Renuse, S., Vanderboom, P. M., Madugundu, A. K., Budhraja, R., McAulay, K., Grys, T. E., Rule, A. D., et al. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.1c00391 · Cited by 41

Optimal conditions for carrying out trypsin digestions on complex proteomes: From bulk samples to single cells

Mansuri, M. S., Bathla, S., Lam, T. T., Nairn, A. C., & Williams, K. R. (2024) · Journal of Proteomics · doi:10.1016/j.jprot.2024.105109 · Cited by 37

Interindividual variability in gut microbiome mediates the efficacy of resistant starch on MASLD

Long, X., Wang, H., Lu, Y., Gao, X., Xiao, Y., Zhang, M., Guo, J., Yang, H. J., Zhang, R., Li, Q., et al. (2025) · Cell Metabolism · doi:10.1016/j.cmet.2025.10.017 · Cited by 37

Isolation Window Optimization of Data-Independent Acquisition Using Predicted Libraries for Deep and Accurate Proteome Profiling

Doellinger, J., Blumenscheit, C., Schneider, A., & Lasch, P. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c00994 · Cited by 37

Proteomic analysis of the extracellular matrix of human atherosclerotic plaques shows marked changes between plaque types

Lorentzen, L. G., Yeung, K., Eldrup, N., Eiberg, J., Sillesen, H. H., & Davies, M. J. (2024) · Matrix Biology Plus · doi:10.1016/j.mbplus.2024.100141 · Cited by 36

Boosting MS1-only Proteomics with Machine Learning Allows 2000 Protein Identifications in Single-Shot Human Proteome Analysis Using 5 min HPLC Gradient

Ivanov, M. V., Bubis, J. A., Gorshkov, V., Abdrakhimov, D. A., Kjeldsen, F., & Gorshkov, M. V. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00863 · Cited by 33

Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes

Abele, M., Doll, E. V., Bayer, F. P., Meng, C., Lomp, N., Neuhaus, K., Scherer, S., Küster, B., & Ludwig, C. (2023) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2023.100612 · Cited by 34

AMPK integrates metabolite and kinase-based immunometabolic control in macrophages

Phair, I. R., Nisr, R. B., Howden, A. J. M., Sovakova, M., Alqurashi, N., Foretz, M., Lamont, D., Viollet, B., & Rena, G. (2022) · Molecular Metabolism · doi:10.1016/j.molmet.2022.101661 · Cited by 32

Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format

Chen, Y., Gin, J. W., Wang, Y., de Raad, M., Tan, S., Hillson, N. J., Northen, T. R., Adams, P. D., & Petzold, C. J. (2023) · PLoS ONE · doi:10.1371/journal.pone.0288102 · Cited by 31

Infrared MALDI Mass Spectrometry with Laser-Induced Postionization for Imaging of Bacterial Colonies

Brockmann, E. U., Potthoff, A., Tortorella, S., Soltwisch, J., & Dreisewerd, K. (2021) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.1c00020 · Cited by 30

Pump‐Less, Recirculating Organ‐on‐Chip (rOoC) Platform to Model the Metabolic Crosstalk between Islets and Liver

Aizenshtadt, A., Wang, C., Abadpour, S., Menezes, P. D., Wilhelmsen, I., Dalmao‐Fernández, A., Stokowiec, J., Golovin, A., Johnsen, M., Combriat, T. M. D., et al. (2024) · Advanced Healthcare Materials · doi:10.1002/adhm.202303785 · Cited by 35

Targeted degradation of endogenous YAP by nanobody bioPROTAC inhibits tumor progression

Zhou, R., Wang, H., Zhang, G., Liu, Y., Liu, X., Li, Z., Shi, G., Yuan, J., Qu, C., Li, Y., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-64426-7 · Cited by 28

Advances in the proteomic profiling of the matrisome and adhesome

Krásný, L., & Huang, P. H. (2021) · Expert Review of Proteomics · doi:10.1080/14789450.2021.1984885 · Cited by 26

Increasing Proteome Depth While Maintaining Quantitative Precision in Short-Gradient Data-Independent Acquisition Proteomics

Doellinger, J., Blumenscheit, C., Schneider, A., & Lasch, P. (2023) · Journal of Proteome Research · doi:10.1021/acs.jproteome.3c00078 · Cited by 26

Lyotropic Liquid Crystalline Phase Nanostructure and Cholesterol Enhance Lipid Nanoparticle Mediated mRNA Transfection in Macrophages

Iscaro, J., Yu, H., Martínez, N. P., Subramaniam, S., Joyce, P., Wang, H., Dyett, B., White, J., Prestidge, C. A., Drummond, C. J., et al. (2024) · Advanced Functional Materials · doi:10.1002/adfm.202405286 · Cited by 25

Differences in the cerebral amyloid angiopathy proteome in Alzheimer’s disease and mild cognitive impairment

Leitner, D., Kavanagh, T., Kanshin, E., Balcomb, K., Pires, G., Thierry, M., Suazo, J. I., Schneider, J. A., Ueberheide, B. M., Drummond, E., et al. (2024) · Acta Neuropathologica · doi:10.1007/s00401-024-02767-1 · Cited by 30

Sample Preparation for Multi‐Omics Analysis: Considerations and Guidance for Identifying the Ideal Workflow

Woodland, B., Farrell, L. A., Brockbals, L., Rezcallah, M. C., Brennan, A., Sunnucks, E. J., Gould, S. T., Stanczak, A. M., O’Rourke, M. B., & Padula, M. P. (2025) · PROTEOMICS · doi:10.1002/pmic.13983 · Cited by 26

Development of an efficient, effective, and economical technology for proteome analysis

Martin, K. R., Le, H. T., Abdelgawad, A., Yang, C., Lu, G., Keffer, J. L., Zhang, X., Zhuang, Z., Asare‐Okai, P. N., Chan, C. S., et al. (2024) · Cell Reports Methods · doi:10.1016/j.crmeth.2024.100796 · Cited by 23

Deep Time Course Proteomics of SARS-CoV- and SARS-CoV-2-Infected Human Lung Epithelial Cells (Calu-3) Reveals Strong Induction of Interferon-Stimulated Gene Expression by SARS-CoV-2 in Contrast to SARS-CoV

Grossegesse, M., Bourquain, D. R., Neumann, M., Schaade, L., Schulze, J., Mache, C., Wolff, T., Nitsche, A., & Doellinger, J. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.1c00783 · Cited by 21

Spotlight on alternative frame coding: Two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection

Kreitmeier, M., Ardern, Z., Abele, M., Ludwig, C., Scherer, S., & Neuhaus, K. (2022) · iScience · doi:10.1016/j.isci.2022.103844 · Cited by 25

Perchlorate‐specific proteomic stress responses of Debaryomyces hansenii could enable microbial survival in Martian brines

Heinz, J., Doellinger, J., Maus, D., Schneider, A., Lasch, P., Grossart, H., & Schulze‐Makuch, D. (2022) · Environmental Microbiology · doi:10.1111/1462-2920.16152 · Cited by 23

Improving Peptide-Level Mass Spectrometry Analysis via Double Competition

Lin, A., Short, T., Noble, W. S., & Keich, U. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00282 · Cited by 22

Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant

Lin, A., Plubell, D. L., Keich, U., & Noble, W. S. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.1c00483 · Cited by 21

Silence as a way of niche adaptation: mecC-MRSA with variations in the accessory gene regulator (agr) functionality express kaleidoscopic phenotypes

Huber, C., Stamm, I., Ziebuhr, W., Marincola, G., Bischoff, M., Strommenger, B., Jaschkowitz, G., Marciniak, T., Cuny, C., Witte, W., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-71640-4 · Cited by 23

Advances in the clinical use of metaproteomics

Wolf, M., Schallert, K., Knipper, L., Sickmann, A., Sczyrba, A., Benndorf, D., & Heyer, R. (2023) · Expert Review of Proteomics · doi:10.1080/14789450.2023.2215440 · Cited by 21

Effect of Sample Preparation on the Detection and Quantification of Selected Nuts Allergenic Proteins by LC-MS/MS

Sagu, S. T., Huschek, G., Homann, T., & Rawel, H. M. (2021) · Molecules · doi:10.3390/molecules26154698 · Cited by 20

Composition and abundance of midgut surface proteins in the Asian citrus psyllid, Diaphorina citri

Tavares, C. S., Mishra, R., Ghobrial, P. N., & Bonning, B. C. (2022) · Journal of Proteomics · doi:10.1016/j.jprot.2022.104580 · Cited by 19

Peptides as “better biomarkers”? Value, challenges, and potential solutions to facilitate implementation

Latosińska, A., Frantzi, M., & Siwy, J. (2023) · Mass Spectrometry Reviews · doi:10.1002/mas.21854 · Cited by 19

Proteomic Diversity in Bacteria: Insights and Implications for Bacterial Identification

Abele, M., Soleymaniniya, A., Bayer, F. P., Lomp, N., Doll, E. V., Meng, C., Neuhaus, K., Scherer, S., Wenning, M., Wantia, N., et al. (2025) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2025.100917 · Cited by 20

Unbiased Antimicrobial Resistance Detection from Clinical Bacterial Isolates Using Proteomics

Blumenscheit, C., Pfeifer, Y., Werner, G., John, C., Schneider, A., Lasch, P., & Doellinger, J. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c00594 · Cited by 18

Nitrogen fertilizer rate but not form affects the severity of Fusarium wilt in banana

Orr, R., Dennis, P. G., Wong, Y., Browne, D. J., Cooper, M. M., Birt, H. W. G., Lapis-Gaza, H. R., Pattison, A. B., & Nelson, P. N. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.907819 · Cited by 18

Metabolomic, proteomic, and transcriptomic changes in adults with epilepsy on modified Atkins diet

Leitner, D., Siu, Y., Korman, A., Lin, Z., Kanshin, E., Friedman, D. J., Devore, S., Ueberheide, B. M., Tsirigos, A., Jones, D. R., et al. (2023) · Epilepsia · doi:10.1111/epi.17540 · Cited by 18

Quantitative proteomics and in-cell cross-linking reveal cellular reorganisation during early neuronal differentiation of SH-SY5Y cells

Barth, M., Nienguesso, A. T., Santos, A. N., & Schmidt, C. (2022) · Communications Biology · doi:10.1038/s42003-022-03478-7 · Cited by 20

Brain molecular mechanisms in Rasmussen encephalitis

Leitner, D. F., Lin, Z., Sawaged, Z., Kanshin, E., Friedman, D., Devore, S., Ueberheide, B., Chang, J. W., Mathern, G. W., Anink, J. J., et al. (2023) · Epilepsia · doi:10.1111/epi.17457 · Cited by 17

Development of a GC–MS strategy for the determination of cross-linked proteins in 20th century paint tubes

Lluveras‐Tenorio, A., Orsini, S., Pizzimenti, S., Seppia, S. D., Colombini, M. P., Duce, C., & Bonaduce, I. (2021) · Microchemical Journal · doi:10.1016/j.microc.2021.106633 · Cited by 17

Metabolic disruption impairs ribosomal protein levels, resulting in enhanced aminoglycoside tolerance

Shiraliyev, R., & Orman, M. A. (2024) · eLife · doi:10.7554/elife.94903 · Cited by 24

Multilevel Gene Expression Changes in Lineages Containing Adaptive Copy Number Variants

Spealman, P., de Santana, C., De, T., & Gresham, D. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf005 · Cited by 16

Brain Acetyl-CoA Production and Phosphorylation of Cytoskeletal Proteins Are Targets of CYP46A1 Activity Modulation and Altered Sterol Flux

Mast, N., Petrov, A. M., Prendergast, E., Bederman, I. R., & Pikuleva, I. A. (2021) · Neurotherapeutics · doi:10.1007/s13311-021-01079-6 · Cited by 17

Comprehensive comparison of sample preparation workflows for proteomics

Zheng, W., Yang, P., Sun, C., & Zhang, Y. (2022) · Molecular Omics · doi:10.1039/d2mo00076h · Cited by 17

Genome Sequence of Eubacterium limosum B2 and Evolution for Growth on a Mineral Medium with Methanol and CO2 as Sole Carbon Sources

Pregnon, G., Minton, N. P., & Soucaille, P. (2022) · Microorganisms · doi:10.3390/microorganisms10091790 · Cited by 15

Comparison of the amyloid plaque proteome in Down syndrome, early‐onset Alzheimer's disease, and late‐onset Alzheimer's disease

Martá-Ariza, M., Leitner, D. F., Kanshin, E., Suazo, J., Giusti Pedrosa, A., Thierry, M., Lee, E. B., Devinsky, O., Drummond, E., Fortea, J., et al. (2025) · Acta Neuropathologica · doi:10.1007/s00401-025-02844-z · Cited by 15

Extracellular Matrix Proteomics: The mdx-4cv Mouse Diaphragm as a Surrogate for Studying Myofibrosis in Dystrophinopathy

Dowling, P., Gargan, S., Zweyer, M., Swandulla, D., & Ohlendieck, K. (2023) · Biomolecules · doi:10.3390/biom13071108 · Cited by 16

Raphe and ventrolateral medulla proteomics in epilepsy and sudden unexpected death in epilepsy

Leitner, D., Kanshin, E., Askenazi, M., Faustin, A., Friedman, D. J., Devore, S., Ueberheide, B. M., Wısnıewskı, T., & Devinsky, O. (2022) · Brain Communications · doi:10.1093/braincomms/fcac186 · Cited by 15

“Organ-in-a-Column” Coupled On-line with Liquid Chromatography-Mass Spectrometry

Kogler, S., Aizenshtadt, A., Harrison, S. P., Skottvoll, F. S., Berg, H. E., Abadpour, S., Scholz, H., Sullivan, G. J., Thiede, B., Lundanes, E., et al. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.2c04530 · Cited by 15

Localized proteomic differences in the choroid plexus of Alzheimer's disease and epilepsy patients

Leitner, D., Kanshin, E., Faustin, A., Thierry, M., Friedman, D. J., Devore, S., Ueberheide, B. M., Devinsky, O., & Wısnıewskı, T. (2023) · Frontiers in Neurology · doi:10.3389/fneur.2023.1221775 · Cited by 17

Heat ‘n Beat: A Universal High-Throughput End-to-End Proteomics Sample Processing Platform in under an Hour

Xavier, D., Lucas, N., Williams, S. G., Koh, J. M. S., Ashman, K., Loudon, C., Reddel, R. R., Hains, P. G., & Robinson, P. J. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.3c04708 · Cited by 14

ASAP─Automated Sonication-Free Acid-Assisted Proteomes─from Cells and FFPE Tissues

Barnabas, G. D., Goebeler, V., Tsui, J., Bush, J. W., & Lange, P. F. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.2c04264 · Cited by 13

Addressing Cellular Heterogeneity in Cancer through Precision Proteomics

Waas, M., & Kislinger, T. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00338 · Cited by 13

Quantitative proteome profiling provides evidence of an activation of the complement cascade in ATTR amyloidosis

Treitz, C., Gottwald, J., Gericke, E., Urbán, P., Meliß, R. R., Axmann, H.-D., Siebert, F., Becker, K., Tholey, A., & Röcken, C. (2021) · Amyloid · doi:10.1080/13506129.2021.2015316 · Cited by 13

Comparison of SPEED, S-Trap, and In-Solution-Based Sample Preparation Methods for Mass Spectrometry in Kidney Tissue and Plasma

Templeton, E. M., Pilbrow, A. P., Kleffmann, T., Pickering, J. W., Rademaker, M. T., Scott, N. J. A., Ellmers, L. J., Charles, C. J., Endre, Z. H., Richards, M., et al. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24076290 · Cited by 16

N-Terminal Proteomics Reveals Distinct Protein Degradation Patterns in Different Types of Human Atherosclerotic Plaques

Lorentzen, L. G., Yeung, K., Zitkeviciute, A., Yang-Jensen, K. C., Eldrup, N., Eiberg, J., & Davies, M. J. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00548 · Cited by 16

Clinical Microbiome Analysis by Mass Spectrometry–Based Metaproteomics

Zhang, X., Ning, Z., Mayne, J., & Figeys, D. (2025) · Annual Review of Analytical Chemistry · doi:10.1146/annurev-anchem-071124-113819 · Cited by 15

Daphnia stress response to environmental concentrations of chloramphenicol—multi-omics approach

Grzesiuk, M., Grabska, M., Malinowska, A., Świderska, B., Grzesiuk, E., Garbicz, D., & Gόrecki, A. (2024) · Environmental Science and Pollution Research · doi:10.1007/s11356-024-35045-4 · Cited by 12

Proteomic Analysis of a Rat Streptozotocin Model Shows Dysregulated Biological Pathways Implicated in Alzheimer’s Disease

da Silva, E. M. G., Fischer, J. D. S. D. G., Signorini-Souza, I. D. L., Andrade, A. C. C., Souza, L. C., Andrade, M. K., Carvalho, P. C., de Souza, R. L. R., Vital, M. A. B. F., & Passetti, F. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25052772 · Cited by 12

ZASP: A Highly Compatible and Sensitive ZnCl2 Precipitation-Assisted Sample Preparation Method for Proteomic Analysis

Shao, X., Huang, Y., Xu, R., He, Q., Zhang, M., He, F., & Wang, D. (2024) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2024.100837 · Cited by 11

Coupling proteomics and lipidomics for insights into regulation of oat (Avena sativa) grain lipid synthesis

Lau, W. C. D., Donnellan, L., Harris, J. C., Seidel, J., Hayes, J. E., Croser, J. S., & Hoffmann, P. (2025) · Food Chemistry · doi:10.1016/j.foodchem.2025.143644 · Cited by 11

Simple In-Cell Processing Enables Deep Proteome Analysis of Low-Input Caenorhabditis elegans

Elsayyid, M. W., Tanis, J. E., & Yu, Y. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.4c05003 · Cited by 13

Chemobiosis reveals tardigrade tun formation is dependent on reversible cysteine oxidation

Smythers, A. L., Joseph, K. M., O’Dell, H. M., Clark, T. A., Crislip, J. R., Flinn, B. B., Daughtridge, M. H., Stair, E. R., Mubarek, S. N., Lewis, H. C., et al. (2024) · PLoS ONE · doi:10.1371/journal.pone.0295062 · Cited by 12

Optimisation of Sporosori Purification and Protein Extraction Techniques for the Biotrophic Protozoan Plant Pathogen Spongospora subterranea

Balotf, S., Wilson, R., Tegg, R. S., Nichols, D. S., & Wilson, C. R. (2020) · Molecules · doi:10.3390/molecules25143109 · Cited by 12

Automation of peptide desalting for proteomic liquid chromatography – tandem mass spectrometry by centrifugal microfluidics

Klatt, J.-N., Dinh, T. J., Schilling, O., Zengerle, R., Schmidt, F., Hutzenlaub, T., & Paust, N. (2021) · Lab on a Chip · doi:10.1039/d1lc00137j · Cited by 11

Detection and Quantitation of Small Proteins Using Mass Spectrometry

Franco, P., Zeinert, R., Meier-Credo, J., Storz, G., & Langer, J. D. (2025) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2025.101052 · Cited by 10

Advances in cancer biomarkers: current detection strategies and challenges

Liu, Z., Huang, Z., Chen, X., Zhang, L., Wu, Q. D., Li, L., Yu, C., & Wei, J. (2025) · Coordination Chemistry Reviews · doi:10.1016/j.ccr.2025.217242 · Cited by 10

SPEED-E: A modified version of the sample preparation by Easy extraction and Digestion(-free) protocol for enamel-based sex estimation in archaeological remains

Cleland, T. P., McGuire, S. A., Beatrice, J. S., Moran, K., & France, C. A. M. (2024) · Journal of Archaeological Science · doi:10.1016/j.jas.2024.106006 · Cited by 10

Composition and abundance of midgut plasma membrane proteins in two major hemipteran vectors of plant viruses, Bemisia tabaci and Myzus persicae

Jiménez, J., Mishra, R., Wang, X., Magee, C. M., & Bonning, B. C. (2024) · Archives of Insect Biochemistry and Physiology · doi:10.1002/arch.22133 · Cited by 10

Comparative proteoinformatics revealed the essentials of SDS impact on HaCaT keratinocytes

Shkrigunov, T., Kisrieva, Y. S., Samenkova, N. F., Larina, O. B., Zgoda, V. G., Rusanov, A. L., Romashin, D. D., Luzgina, N. G., Karuzina, I. I., Лисица, А. В., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-25934-4 · Cited by 10

Antifungal activity and identification of bioactive peptide from Etawa crossbreed goat (Capra hircus) milk protein hydrolyzed using trypsin enzyme

Ningsih, D. R., Raharjo, T. J., Haryadi, W., & Wikandari, R. (2023) · Arabian Journal of Chemistry · doi:10.1016/j.arabjc.2023.105249 · Cited by 10

Fully automated sample treatment method for high throughput proteome analysis

Yuan, H., Dai, Z., Zhang, X., Zhao, B., Chu, H., Zhang, L., & Zhang, Y. (2020) · Science China Chemistry · doi:10.1007/s11426-020-9878-8 · Cited by 10

ATTR- and AFib amyloid - two different types of amyloid in the annular ligament of trigger finger

Treitz, C., Müller-Marienburg, N., Meliß, R. R., Urban, P. P., Axmann, H.-D., Siebert, F., Becker, K., Martens, K., Behrens, H., Gericke, E., et al. (2023) · Amyloid · doi:10.1080/13506129.2023.2226298 · Cited by 9

The Antioxidant and Bioactive Potential of Olive Mill Waste

Attard, K., & Lia, F. (2024) · Biochemistry · doi:10.5772/intechopen.1004127 · Cited by 9

ATP-Triggered Fe(CN) 2 CO Synthon Transfer from the Maturase HypCD to the Active Site of Apo-[NiFe]-Hydrogenase

Kwiatkowski, A., Caserta, G., Schulz, A.-C., Frielingsdorf, S., Pelmenschikov, V., Weißer, K., Belsom, A., Rappsilber, J., Sergueev, I., Limberg, C., et al. (2024) · Journal of the American Chemical Society · doi:10.1021/jacs.4c09791 · Cited by 9

Targeted protein degradation in Escherichia coli using CLIPPERs

Izert, M. A., Klimecka, M. M., Antosiewicz, A., Wróblewski, K., Kowalski, J. J., Bandyra, K., Goral, T. K., Kmiecik, S., Serwa, R. A., & Górna, M. W. (2025) · EMBO Reports · doi:10.1038/s44319-025-00510-9 · Cited by 9

In vivo protein turnover rates in varying oxygen tensions nominate MYBBP1A as a mediator of the hyperoxia response

Chen, X., Haribowo, A. G., Baik, A. H., Fossati, A., Stevenson, E. J., Chen, Y. R., Reyes, N. S., Peng, T., Matthay, M. A., Traglia, M., et al. (2023) · Science Advances · doi:10.1126/sciadv.adj4884 · Cited by 10

Stable Isotope-Triggered Offset Fragmentation Allows Massively Multiplexed Target Profiling on Quadrupole-Orbitrap Mass Spectrometers

Grossegesse, M., Hartkopf, F., Nitsche, A., & Doellinger, J. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00065 · Cited by 9

MALDI mass spectrometry imaging unravels organ and amyloid‐type specific peptide signatures in pulmonary and gastrointestinal amyloidosis

Schürmann, J., Gottwald, J., Rottenaicher, G. J., Tholey, A., & Röcken, C. (2021) · PROTEOMICS - CLINICAL APPLICATIONS · doi:10.1002/prca.202000079 · Cited by 9

A novel protocol for in‐depth analysis of recombinant adeno‐associated virus capsid proteins using UHPLC–MS/MS

Zarei, M., Wang, P., Jonveaux, J., Haller, F. M., Gu, B., Koulov, A. V., & Jahn, M. (2021) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.9247 · Cited by 8

Automated Sample Preparation for Mass Spectrometry-Based Clinical Proteomics

Müller, T., Cremonini, M. A., Kliewer, G., & Krijgsveld, J. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3457-8_11 · Cited by 8

Impaired synaptic incorporation of AMPA receptors in a mouse model of fragile X syndrome

Chojnacka, M., Beroun, A., Magnowska, M., Stawikowska, A., Cysewski, D., Miłek, J., Dziembowska, M., & Kuźniewska, B. (2023) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2023.1258615 · Cited by 8

Benchmarking low- and high-throughput protein cleanup and digestion methods for human fecal metaproteomics

Tanca, A., Deledda, M. A., Diego, L. D., Abbondio, M., & Uzzau, S. (2024) · mSystems · doi:10.1128/msystems.00661-24 · Cited by 8

Bap-Independent Biofilm Formation in Staphylococcus xylosus

Schiffer, C. J., Abele, M., Ehrmann, M. A., & Vogel, R. F. (2021) · Microorganisms · doi:10.3390/microorganisms9122610 · Cited by 8

Modulation of Virulence-Associated Traits in Aspergillus fumigatus by BET Inhibitor JQ1

Орехова, А. В., Angelis, M. D., Cacciotti, A., Reverberi, M., Rotili, D., Giorgi, A., Protto, V., Bonincontro, G., Fiorentino, F., Zgoda, V. G., et al. (2022) · Microorganisms · doi:10.3390/microorganisms10112292 · Cited by 8

Gβγ subunits colocalize with RNA polymerase II and regulate transcription in cardiac fibroblasts

Khan, S. M., Martin, R., Bayne, A. N., Pétrin, D., Bourque, K., Jones-Tabah, J., Bouazza, C. A., Blaney, J., Lau, J., Martins-Cannavino, K., et al. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.103064 · Cited by 8

Quantitative detection of hidden milk allergens in hypoallergenic formulas through bottom-up proteomics, high-resolution mass spectrometry and the mechanism of D-ribose in reducing the allergenicity in vitro

Xu, D., Huang, H., Yang, Y., Yue, Y., Zong, L., Liu, Z., Wang, Y., Hu, W., Liu, X., & Yang, J. (2025) · LWT · doi:10.1016/j.lwt.2025.117446 · Cited by 7

The Escherichia coli replication initiator DnaA is titrated on the chromosome

Olivi, L., Köstlbacher, S., Ludwig, C., Langendoen, M., Claassens, N. J., Ettema, T. J. G., van der Oost, J., ten Wolde, P. R., Hohlbein, J., & Staals, R. H. J. (2025) · Nature Communications · doi:10.1038/s41467-025-63147-1 · Cited by 7

Polymeric-lipid nanoparticles that leverage cationic helper lipids and the protein corona for lung-targeted delivery of a novel anti-cancer drug

Subramaniam, S., Donnellan, L., Wignall, A. D., Woodcock, J. M., Coolen, C., Pitson, S. M., Taheri, A., Young, C., Hoffmann, P., Prestidge, C. A., et al. (2025) · Journal of Controlled Release · doi:10.1016/j.jconrel.2025.114299 · Cited by 7

Discovery of Chemical Tools for Polysorbate-Degradative Enzyme Control in the Biopharmaceutical Upstream Process via Multi-Omic Profiling of Host Cell Clones

Tsukidate, T., Sahoo, A., Pendyala, G., Yang, R., Welch, J., Madabhushi, S. R., & Li, X. (2025) · ACS Chemical Biology · doi:10.1021/acschembio.5c00081 · Cited by 6

Tandem mass tag-based proteomics for studying the effects of a biotechnologically produced oyster mushroom against hepatic steatosis in obese Zucker rats

Maheshwari, G., Wen, G., Geßner, D. K., Ringseis, R., Lochnit, G., Eder, K., Zorn, H., & Timm, T. (2021) · Journal of Proteomics · doi:10.1016/j.jprot.2021.104255 · Cited by 7

Antibody responses to dietary antigens are accompanied by specific plasma cells in the infant thymus

Cordero, H., Hess, J., Nitschki, E., Kanshin, E., Roy, P., Shihab, R. R., Kalfa, D. M., BACHA, E. A., Ueberheide, B. M., & Zorn, E. (2023) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2023.06.018 · Cited by 7

Precursor deconvolution error estimation: The missing puzzle piece in false discovery rate in top‐down proteomics

Jeong, K., Kaulich, P. T., Jung, W., Kim, J., Tholey, A., & Kohlbacher, O. (2023) · PROTEOMICS · doi:10.1002/pmic.202300068 · Cited by 8

通过易于提取和消化（速度） - 一种基于酸提取的蛋白质组学的通用，快速和可污染方案的样品制备 -

Doellinger, J., 安迪施奈德, Hoeller, M., & 彼得拉索克 (2020)

Comparison of SPEED, S-Trap, and In-Solution-Based Sample Preparation Methods for Mass Spectrometry in Kidney Tissue and Plasma

Templeton, E. M., Pilbrow, A. P., Kleffmann, T., Pickering, J. W., Rademaker, M. T., Scott, N. J. A., Ellmers, L. J., Charles, C. J., Endre, Z. H., Richards, M., et al. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24076290 · Cited by 16

Development of an Automated, High‐throughput Sample Preparation Protocol for Proteomics Analysis

Arul, A. B., Byambadorj, M., Han, N., Park, J. M., & Lee, H. (2015) · Bulletin of the Korean Chemical Society · doi:10.1002/bkcs.10338 · Cited by 14

Solid-Phase Extraction Capture (SPEC) in nanoliter volumes for fast, robust and ultra-sensitive proteomicsPreprint

Heymann, T., Oliinyk, D., Henneberg, L. T., Rodriguez, E. H., Bardziukova, A., Oeller, M., Murgia, M., Olsen, J. V., Stoychev, S., Bache, N., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.31.657165 · Cited by 6

Single-pot, solid-phase-enhanced sample preparation for proteomics experiments

Hughes, C. S., Moggridge, S., Müller, T., Sorensen, P. H. B., Morin, G. B., & Krijgsveld, J. (2018) · Nature Protocols · doi:10.1038/s41596-018-0082-x · Cited by 1,997