Protein Contaminants Matter: Building Universal Protein Contaminant Libraries for DDA and DIA Proteomics

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

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A cross-platform toolkit for mass spectrometry and proteomics

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Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

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DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput

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

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PHD1 controls muscle mTORC1 in a hydroxylation-independent manner by stabilizing leucyl tRNA synthetase

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The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

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Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

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The minimum information about a proteomics experiment (MIAPE)

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OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

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Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry

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Sage: An Open-Source Tool for Fast Proteomics Searching and Quantification at Scale

Lazear, M. R. (2023) · Journal of Proteome Research · doi:10.1021/acs.jproteome.3c00486 · Cited by 93

Expanding the human proteome with microproteins and peptideins

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A framework for ultra-low-input spatial tissue proteomics

Makhmut, A., Qin, D., Fritzsche, S., Nimo, J., König, J., & Coscia, F. (2023) · Cell Systems · doi:10.1016/j.cels.2023.10.003 · Cited by 67

High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles

Coupland, C. E., Karimi, R., Bueler, S. A., Liang, Y., Courbon, G. M., Di Trani, J. M., Wong, C. J., Saghian, R., Youn, J.-Y., Wang, L.-Y., et al. (2024) · Science · doi:10.1126/science.adp5577 · Cited by 58

Multi-modal proteomic characterization of lysosomal function and proteostasis in progranulin-deficient neurons

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Unifying the analysis of bottom-up proteomics data with CHIMERYS

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Universal Pretreatment Development for Low-input Proteomics Using Lauryl Maltose Neopentyl Glycol

Konno, R., Ishikawa, M., Nakajima, D., Endo, Y., Ohara, O., & Kawashima, Y. (2024) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2024.100745 · Cited by 42

Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics

Biggs, G. S., Cawood, E. E., Vuorinen, A., McCarthy, W. J., Wilders, H., Riziotis, I. G., van der Zouwen, A. J., Pettinger, J., Nightingale, L., Chen, P., et al. (2025) · Nature Communications · doi:10.1038/s41467-024-55057-5 · Cited by 36

Spatial multiomics of acute myocardial infarction reveals immune cell infiltration through the endocardium

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C-terminal amides mark proteins for degradation via SCF–FBXO31

Muhar, M., Farnung, J., Cernakova, M., Hofmann, R., Henneberg, L. T., Pfleiderer, M. M., Denoth‐Lippuner, A., Kalčic, F., Nievergelt, A. S., al‐Bayati, M., et al. (2025) · Nature · doi:10.1038/s41586-024-08475-w · Cited by 34

Challenges of MS‐based small extracellular vesicles proteomics

Fochtman, D., Marczak, Ł., Pietrowska, M., & Wojakowska, A. (2024) · Journal of Extracellular Vesicles · doi:10.1002/jev2.70020 · Cited by 33

Detection of the Arabidopsis Proteome and Its Post-translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas

van Wijk, K. J., Leppert, T., Sun, Z., Kearly, A., Li, M., Mendoza, L., Guzchenko, I., Debley, E. L., Sauermann, G., Routray, P., et al. (2023) · Journal of Proteome Research · doi:10.1021/acs.jproteome.3c00536 · Cited by 30

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

An Automated and Fast Sample Preparation Workflow for Laser Microdissection Guided Ultrasensitive Proteomics

Makhmut, A., Qin, D., Hartlmayr, D., Seth, A., & Coscia, F. (2024) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2024.100750 · Cited by 27

Proteomics—The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience

Coorssen, J. R., & Padula, M. P. (2024) · Proteomes · doi:10.3390/proteomes12020014 · Cited by 28

Cellular internalization pathways of environmentally exposed microplastic particles: Phagocytosis or macropinocytosis?

Ramsperger, A. F. R. M., Wieland, S., Wilde, M. V., Fröhlich, T., Kress, H., & Laforsch, C. (2025) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2025.137647 · Cited by 25

Peptidomics profiling and biological activities of grape pomace protein hydrolysates

Knuf, F., Caspers-Weiffenbach, R., Schieber, A., & Fontana, A. (2024) · Food Chemistry · doi:10.1016/j.foodchem.2024.141032 · Cited by 23

Cylicins are a structural component of the sperm calyx being indispensable for male fertility in mice and human

Schneider, S., Kovacevic, A., Mayer, M., Dicke, A., Arévalo, L., Koser, S. A., Hansen, J. N., Young, S., Brenker, C., Kliesch, S., et al. (2023) · eLife · doi:10.7554/elife.86100 · Cited by 23

OmicScope unravels systems-level insights from quantitative proteomics data

Reis‐de‐Oliveira, G., Carregari, V. C., de Sousa, G. R. D. R., & Martins‐de‐Souza, D. (2024) · Nature Communications · doi:10.1038/s41467-024-50875-z · Cited by 23

Supramolecular self-assembly strategies of natural-based β-lactoglobulin modulating bitter perception of goat milk–derived bioactive peptides

Zhang, R., & Jia, W. (2024) · Journal of Dairy Science · doi:10.3168/jds.2023-24386 · Cited by 22

AlphaPeptStats: an open-source Python package for automated and scalable statistical analysis of mass spectrometry-based proteomics

Krismer, E., Bludau, I., Strauss, M. T., & Mann, M. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad461 · Cited by 22

Environment modulates protein heterogeneity through transcriptional and translational stop codon readthrough

Romero, M. L. R., Poehls, J., Kirilenko, A., Richter, D., Jumel, T., Shevchenko, A., & Tóth-Petróczy, Á. (2024) · Nature Communications · doi:10.1038/s41467-024-48387-x · Cited by 21

TIMS 2 Rescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MS 2 Rescore

Declercq, A., Devreese, R., Scheid, J., Jachmann, C., Bossche, T. V. D., Preikschat, A., Gomez‐Zepeda, D., Rijal, J. B., Hirschler, A., Krieger, J. R., et al. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00609 · Cited by 20

Proteomic insights into mental health status: plasma markers in young adults

Afonin, A. М., Piironen, A., Maciel, I. D. S., Ivanova, M., Alatalo, A., Whipp, A. M., Pulkkinen, L., Rose, R. J., KAMP, I. V., Kaprio, J. A., et al. (2024) · Translational Psychiatry · doi:10.1038/s41398-024-02751-z · Cited by 24

In-depth analysis of data characteristics and comparative evaluation of dda and dia accuracy in label-free quantitative proteomics of biological samples

Zou, X., Wang, L., Chen, Y., Fu, H., Gao, Y., Liu, B., Tan, M., & Zhai, L. (2025) · Clinical Proteomics · doi:10.1186/s12014-025-09572-2 · Cited by 19

Plasma proteomics discovery of mental health risk biomarkers in adolescents

Maciel, I. D. S., Piironen, A., Afonin, A. М., Ivanova, M., Alatalo, A., Jadhav, K. K., Júlvez, J., Foraster, M., KAMP, I. V., & Kanninen, K. M. (2023) · Nature Mental Health · doi:10.1038/s44220-023-00103-2 · Cited by 21

Multiomics Evaluation of Human iPSCs and iPSC-Derived Neurons

Lee, G. B., Mazli, W. N. A. B., & Hao, L. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.3c00790 · Cited by 20

An integrated workflow for quantitative analysis of the newly synthesized proteome

Borteçen, T., Müller, T., & Krijgsveld, J. (2023) · Nature Communications · doi:10.1038/s41467-023-43919-3 · Cited by 19

Plasma-Derived Extracellular Vesicle Proteomics

Tan, Y., Kao, W., Boppart, M. D., & Sweedler, J. V. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5c00316 · Cited by 18

A Bioconductor workflow for processing, evaluating, and interpreting expression proteomics data

Hutchings, C., Dawson, C. S., Krueger, T., Lilley, K. S., & Breckels, L. M. (2023) · F1000Research · doi:10.12688/f1000research.139116.1 · Cited by 18

Combining Data Independent Acquisition With Spike-In SILAC (DIA-SiS) Improves Proteome Coverage and Quantification

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Disclosing the molecular profile of the human amniotic mesenchymal stromal cell secretome by filter-aided sample preparation proteomic characterization

Muntiu, A., Papait, A., Vincenzoni, F., Vitali, A., Lattanzi, W., Romele, P., Cargnoni, A., Silini, A. R., Parolini, O., & Desiderio, C. (2023) · Stem Cell Research & Therapy · doi:10.1186/s13287-023-03557-4 · Cited by 18

Common viral infections inhibit egg laying in honey bee queens and are linked to premature supersedure

Chapman, A., McAfee, A., Tarpy, D. R., Fine, J. D., Rempel, Z., Peters, K., Currie, R., & Foster, L. J. (2024) · Scientific Reports · doi:10.1038/s41598-024-66286-5 · Cited by 16

Classification of Collagens via Peptide Ambiguation, in a Paleoproteomic LC-MS/MS-Based Taxonomic Pipeline

Engels, I., Burnett, A., Robert, P., Pironneau, C., Abrams, G., Bouwmeester, R., der Plaetsen, P. V., Modica, K. D., Otte, M., Straus, L. G., et al. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00962 · Cited by 17

Electrophilic compound screening identifies GPX4-dependent ferroptosis as a senescence vulnerability

D’Ambrosio, M., White, M. E. H., Gavriil, E.-S., Bousset, L., Birch, J., Gruevska, A., Pasquini, E., Colucci, M., Fong, W., Mosole, S., et al. (2026) · Nature Cell Biology · doi:10.1038/s41556-026-01921-z · Cited by 17

The spatial proteome of the Plasmodium falciparum schizont illuminates the composition and evolutionary trajectories of its organelles

Chisholm, S. A., Flores, V., Kemp, A., Breckels, L., Koreny, L., Pacheco, N. D. S., Barylyuk, K., Kuroshchenkova, A., Lilley, K. S., Rayner, J., et al. (2025) · bioRxiv · doi:10.1038/s41467-026-73664-2 · Cited by 15

Macrophage-induced enteric neurodegeneration leads to motility impairment during gut inflammation

Breßer, M., Siemens, K. D., Schneider, L. H., Lunnebach, J. E., Leven, P., Glowka, T. R., Oberländer, K., Domenico, E. D., Schultze, J. L., Schmidt, J., et al. (2025) · EMBO Molecular Medicine · doi:10.1038/s44321-024-00189-w · Cited by 15

Enhanced Production of Rebaudioside D and Rebaudioside M through V155T Substitution in the Glycosyltransferase UGT91D2 from Stevia rebaudiana

Shoji, T., Tanaka, Y., Nakashima, Y., Mizohata, E., Komaki, M., Sugawara, S., Takaya, J., Yonekura‐Sakakibara, K., Morita, H., Saito, K., et al. (2025) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.4c09392 · Cited by 15

Thermal inkjet makes label-free single-cell proteomics accessible and easy

Stanisheuski, S., Ebrahimi, A., Vaidya, K. A., Jang, H. S., Yang, L., Eddins, A. J., Marean‐Reardon, C. L., Franco, M. C., & Maier, C. S. (2024) · Frontiers in Chemistry · doi:10.3389/fchem.2024.1428547 · Cited by 14

Deep Profiling of the Proteome Dynamics of Pseudomonas aeruginosa Reference Strain PAO1 under Different Growth Conditions

Hou, M., Huang, J., Jia, T., Guan, Y., Yang, F., Zhou, H., Huang, P., Wang, J., Yang, L., & Dai, L. (2023) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00785 · Cited by 14

Functionally redundant formate dehydrogenases enable formate-dependent growth in Methanococcus maripaludis

Halim, M. F. A., Fonseca, D. R., Niehaus, T. D., & Costa, K. C. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.105550 · Cited by 13

Proteomic Characterization of 1000 Human and Murine Neutrophils Freshly Isolated From Blood and Sites of Sterile Inflammation

Ghosh, S., Tuz, A. A., Stenzel, M., Singh, V., Richter, M., Soehnlein, O., Lange, E., Heyer, R., Cibir, Z., Beer, A., et al. (2024) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2024.100858 · Cited by 13

Screening of wine industry by-products as a source of bioactive peptides: Fractionation, in vitro antihypertensive activity and peptidomics analysis

Fontana, A., Knuf, F., Monasterio, R. P., & Schieber, A. (2025) · Food Chemistry · doi:10.1016/j.foodchem.2025.143478 · Cited by 13

Tyrosyl-DNA phosphodiesterase 1 excises the 3′-DNA-ALKBH1 cross-link and its application for 3′-DNA-ALKBH1 cross-link characterization by LC-MS/MS

Wei, X., Person, M. D., & Yang, K. (2022) · DNA repair · doi:10.1016/j.dnarep.2022.103391 · Cited by 13

Identification of MIMAS, a multifunctional mega-assembly integrating metabolic and respiratory biogenesis factors of mitochondria

Horten, P., Song, K., Garlich, J., Hardt, R., Colina-Tenorio, L., Horvath, S. E., Schulte, U., Fakler, B., van der Laan, M., Becker, T., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.113772 · Cited by 12

Extracellular Vesicles from Highly Metastatic Osteosarcoma Cells Induce Pro‐Tumorigenic Macrophage Phenotypes

Griffin, K. H., Mizenko, R. R., Arun, V., Carney, R. P., & Leach, J. K. (2024) · Advanced Biology · doi:10.1002/adbi.202300577 · Cited by 12

Pharmacogene expression during progression of metabolic dysfunction-associated steatotic liver disease: Studies on mRNA and protein levels and their relevance to drug treatment

Govaere, O., Cockell, S., Zatorska, M., Wonders, K., TINIAKOS, D. G., Frey, A. M., Palmowski, P., Walker, R., Porter, A., Trost, M., et al. (2024) · Biochemical Pharmacology · doi:10.1016/j.bcp.2024.116249 · Cited by 12

Mass spectrometry–based proteomic exploration of diverse murine macrophage cellular models

Gudgeon, J., Dannoura, A., Chatterjee, R., Sidgwick, F. R., Raymond, B. B. A., Frey, A. M., Marín‐Rubio, J. L., & Trost, M. (2024) · Life Science Alliance · doi:10.26508/lsa.202402760 · Cited by 12

CCDC134 controls TLR biogenesis through the ER chaperone Gp96

Bernaleau, L., Drobek, M., Blank, F., Walch, P., Delacrétaz, M., Drobek, A., Tortajada, M., Brož, P., Majer, O., & Rebsamen, M. (2024) · The Journal of Experimental Medicine · doi:10.1084/jem.20240825 · Cited by 12

Spatial proteomics of ovarian cancer precursors delineates early disease changes and drug targets

Makhmut, A., Dragomir, M. P., Fritzsche, S., Möbs, M., Schmitt, W., TAUBE, E. T., & Coscia, F. (2025) · Molecular Systems Biology · doi:10.1038/s44320-025-00168-4 · Cited by 12

Integration of data‐independent acquisition (DIA) with co‐fractionation mass spectrometry (CF‐MS) to enhance interactome mapping capabilities

Hay, B. N., Akinlaja, M. O., Baker, T. C., Houfani, A. A., Stacey, R. G., & Foster, L. J. (2023) · PROTEOMICS · doi:10.1002/pmic.202200278 · Cited by 11

Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome

Lee, E. M., Srinivasan, S., Purvine, S. O., Fiedler, T. L., Leiser, O. P., Proll, S. C., Minot, S. S., Kaiser, B. L. D., & Fredricks, D. N. (2023) · mSystems · doi:10.1128/msystems.00678-22 · Cited by 12

Chickpea Proteome Analysis Reveals Genotype-Dependent Variations Associated with Seed Traits

Bose, U., Buck, S., Sirault, X. R. R., Bahmani, M., Byrne, K. A., Stockwell, S., McWilliam, S. M., Colgrave, M. L., Juhász, A., & Ral, J.-P. F. (2024) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.4c07669 · Cited by 11

Overcoming Analytical Challenges in Proximity Labeling Proteomics

Li, H., Mazli, W. N. A. B., & Hao, L. (2025) · Journal of Mass Spectrometry · doi:10.1002/jms.5134 · Cited by 11

Characterization of Spirulina‐derived extracellular vesicles and their potential as a vaccine adjuvant

Sharifpour, M. F., Sıkder, S., Wong, Y., Koifman, N., Thomas, T., Courtney, R. L., Seymour, J., & Loukas, A. C. (2024) · Journal of Extracellular Biology · doi:10.1002/jex2.70025 · Cited by 10

Proteomic characterization and comparison of the infective and adult life stage secretomes from Necator americanus and Ancylostoma ceylanicum

Wong, Y., Rosa, B. A., Becker, L., Camberis, M., Gros, G. S. L., Zhan, B., Bottazzi, M. E., Fujiwara, R. T., Ritmejerytė, E., Laha, T., et al. (2025) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0012780 · Cited by 10

Structure of a distinct β-barrel assembly machinery complex in the Bacteroidota

(2025) · doi:10.1038/s41564-025-02132-2 · Cited by 10

pepDESC: A Method for the Detection of Differentially Expressed Proteins for Mass Spectrometry-Based Single-Cell Proteomics Using Peptide-level Information

Zhang, Y. (2023) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2023.100583 · Cited by 10

Factors affecting heat resilience of drone honey bees (Apis mellifera) and their sperm

McAfee, A., Metz, B. N., Connor, P., Du, K., Allen, C. W., Frausto, L. A., Swenson, M. P., Phillips, K. S., Julien, M., Rempel, Z., et al. (2025) · PLoS ONE · doi:10.1371/journal.pone.0317672 · Cited by 9

Benchmarking SILAC Proteomics Workflows and Data Analysis Platforms

Frankenfield, A. M., Yang, K., Mazli, W. N. A. B., Shih, J., Yu, F., Lo, E., Nesvizhskii, A. I., & Hao, L. (2025) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2025.100980 · Cited by 9

CHIP protects lysosomes from CLN4 mutant-induced membrane damage

Lee, J., Chin, N. Y., Zou, J., Mazli, W. N. A. B., Jarník, M., Saidi, L. F., Xu, Y., Jeong, E., Suh, J., Replogle, J. M., et al. (2025) · Nature Cell Biology · doi:10.1038/s41556-025-01738-2 · Cited by 9

Lipid nanoparticle-based non-viral in situ gene editing of congenital ichthyosis-causing mutations in human skin models

Apaydin, D. C., Sadhnani, G., Carlaw, T., Renziehausen, J., Lizunova, E., Filor, V., Hiller, A. L., Brumhard, S., Halim, V., Brüning, U., et al. (2026) · Cell stem cell · doi:10.1016/j.stem.2026.01.001 · Cited by 10

Advancing Sustainable Malting Practices: Aquaporins as Potential Breeding Targets for Improved Water Uptake during Controlled Germination of Barley (Hordeum vulgare L.)

O’Lone, C. E., Juhász, A., Nye‐Wood, M. G., Moody, D., Dunn, H., Ral, J.-P. F., & Colgrave, M. L. (2024) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.4c00884 · Cited by 9

MS Ana: Improving Sensitivity in Peptide Identification with Spectral Library Search

Dorl, S., Winkler, S., Mechtler, K., & Dorfer, V. (2023) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00658 · Cited by 9

Role of ZFHX4 in orofacial clefting based on human genetic data and zebrafish models

Ishorst, N., Hölzel, S., Greve, C., Yilmaz, Ö., Lindenberg, T. T., Lambertz, J., Drichel, D., Zametica, B., Mingardo, E., Kalanithy, J. C., et al. (2024) · European Journal of Human Genetics · doi:10.1038/s41431-024-01775-9 · Cited by 8

Localization of Organelle Proteins Using Data-Independent Acquisition (DIA-LOP)

McCaskie, K. J. A., Hutchings, C., Feret, R., Kim, Y.-I., Breckels, L. M., Deery, M. J., & Lilley, K. S. (2025) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2025.101047 · Cited by 8

An Ultrasensitive Spatial Tissue Proteomics Workflow Exceeding 100 Proteomes Per Day

Klingeberg, M., Krisp, C., Fritzsche, S., Schallenberg, S., Hornburg, D., & Coscia, F. (2025) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2025.101489 · Cited by 8

Investigating trade-offs between ovary activation and immune protein expression in bumble bee ( Bombus impatiens ) workers and queens

McAfee, A., Chapman, A., Bao, G., Tarpy, D. R., & Foster, L. J. (2024) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2023.2463 · Cited by 8

Contaminant Spot Check and Removal Assay (ContamSPOT) for Mass Spectrometry Analysis

Smeriglio, N., Li, H., Mazli, W. N. A. B., Bendel, K., & Hao, L. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.3c05020 · Cited by 8

Proteomic Analysis Reveals Trilaciclib-Induced Senescence

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Proteomic exploration reveals a metabolic rerouting due to low oxygen during controlled germination of malting barley (Hordeum vulgare L.)

O’Lone, C. E., Juhász, A., Nye‐Wood, M. G., Dunn, H., Moody, D. B., Ral, J.-P. F., & Colgrave, M. L. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2023.1305381 · Cited by 8

ProteoBench: the community-curated platform for comparing proteomics data analysis workflowsPreprint

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Praja2 controls P-body assembly and translation in glioblastoma by non-proteolytic ubiquitylation of DDX6

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Characterization of Neuronal Lysosome Interactome with Proximity Labeling Proteomics

Frankenfield, A. M., Ni, J., & Hao, L. (2022) · Journal of Visualized Experiments · doi:10.3791/64132 · Cited by 7

Ganglioglioma cells potentiate neuronal network synchronicity and elicit burst discharges via released factors

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Differences in Uniquely Identified Peptides Between ddaPASEF and diaPASEF

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Quantitative Proteomics and Phosphoproteomics Analysis of Patient-Derived Ovarian Cancer Stem Cells

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Multi-omics insights into the response of Aspergillus parasiticus to long-chain alkanes in relation to polyethylene modification

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A conserved chronobiological complex times C. elegans development

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Secreted and surface proteome and transcriptome of Opisthorchis felineus

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Dose-dependent CHCHD10 dysregulation dictates motor neuron disease severity and alters creatine metabolism

Harjuhaahto, S., Jokela, M. E., Rajendran, J., Rokka, M., Hu, B., Kvist, J., Zhang, F., Zárybnický, T., Haimilahti, K., Euro, L., et al. (2025) · Acta Neuropathologica Communications · doi:10.1186/s40478-025-02039-3 · Cited by 6

Differential effects of age and sex on tau pathology propagation in the htau mouse model: A neuropathological and proteomic study

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CRL2FEM1B uses heme to recruit BACH1 for degradation and regulate ferroptosis in lung cancer

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The Peptonizer2000: Bringing Confidence to Metaproteomics

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Porcine ex-vivo intestinal mucus has age-dependent blocking activity against transmissible gastroenteritis virus

Saleem, W., Carpentier, N., Hinnekens, C., Oh, D., Vlierberghe, S. V., Braeckmans, K., & Nauwynck, H. (2024) · Veterinary Research · doi:10.1186/s13567-024-01374-y · Cited by 8

Altered proteomics in brain extracellular vesicles from depressed individuals who died by suicide implicates synaptic processes

Ibrahim, P., Mitsuhashi, H., Taylor, L., Cleyle, J., Mechawar, N., Nagy, C., & Turecki, G. (2025) · The International Journal of Neuropsychopharmacology · doi:10.1093/ijnp/pyaf012 · Cited by 6

Dissecting Branch-Specific Unfolded Protein Response Activation in Drug-Tolerant BRAF-Mutant Melanoma Using Data-Independent Acquisition Mass Spectrometry

Barny, L. A., Hermanson, J. N., Garcia, S. K., Stauffer, P. E., & Plate, L. (2025) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2025.101036 · Cited by 6

A stabilized MERS-CoV spike ferritin nanoparticle vaccine elicits robust and protective neutralizing antibody responses

Powell, A. E., Caruso, H., Park, S., Chen, J., O’Rear, J., Ferrer, B., Stieh, D. J., Weiss, A. M., Belnap, D. M., Walker, A. E., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-68458-5 · Cited by 6

An updated Bioconductor workflow for correlation profiling subcellular proteomics

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PARP7 is a proteotoxic stress sensor that labels proteins for degradation

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Postmortem interval estimation through skeletal muscle protein degradation: a comprehensive review

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Conserved and Unique Protein Expression Patterns Across Reproductive Stage Transitions in Social Hymenopteran Queens

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Proteomics-Based Analysis of Laser-Capture Micro-dissected, Formalin-Fixed Paraffin-Embedded Tissue Samples

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4D-DIA Proteomics Uncovers New Insights into Host Salivary Response Following SARS-CoV-2 Omicron Infection

de Lima, I. L., Cataldi, T. R., Brites, C. R., Labate, M. T. V., Vaz, S. N., Deminco, F., da Cunha, G. S., Labate, C. A., & Eberlin, M. N. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00630 · Cited by 5

Considerations and Software for Successful Immune Cell Deconvolution Using Proteomics Data

Zamore, M., Mosquim, S., Andree, S. L., Altunbulakli, C., Lindstedt, M., & Levander, F. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00868 · Cited by 5

Elucidating the enzymatic response of the white rot basidiomycete Abortiporus biennis for the downgrade of polystyrene

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A comparative study of data‐dependent acquisition and data‐independent acquisition in proteomics analysis of clinical lung cancer tissues constrained by blood contamination

Su, T., Zhong, Y., Zeng, W., Zhang, Y., Wang, S., Cheng, J., Yang, H., Wei, Y., & Gong, M. (2021) · PROTEOMICS - CLINICAL APPLICATIONS · doi:10.1002/prca.202000099 · Cited by 9

Protein Biomarker Discovery in Non-depleted Serum by Spectral Library-Based Data-Independent Acquisition Mass Spectrometry

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DIA proteomics data from a UPS1-spiked E.coli protein mixture processed with six software tools

Gotti, C., Roux‐Dalvai, F., Joly-Beauparlant, C., Mangnier, L., Leclercq, M., & Droit, A. (2022) · Data in Brief · doi:10.1016/j.dib.2022.107829 · Cited by 11

Identification of contaminants in proteomics mass spectrometry data

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DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics

Midha, M. K., Campbell, D. S., Kapil, C., Kusebauch, U., Hoopmann, M. R., Bader, S. L., & Moritz, R. L. (2020) · Nature Communications · doi:10.1038/s41467-020-18901-y · Cited by 44