MS-GF+ makes progress towards a universal database search tool for proteomics

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1. Profiling How the Gut Microbiome Modulates Host Xenobiotic Metabolism in Response to Benzo[a]pyrene and 1-Nitropyrene Exposure
   Whitney L. Garcia, Carson J. Miller, Gerard X. Lomas, Kari A. Gaither, Kimberly J. Tyrrell, Jordan Ned Smith, Kristoffer R. Brandvold, Aaron Wright · 2022 · Chemical Research in Toxicology
2. 40S hnRNP particles are a novel class of nuclear biomolecular condensates
   Michal Domanski, Emil Dedic, Maria Escura Pérez, Antoine Cléry, Sébastien Campagne, Anne‐Christine Uldry, Sophie Braga, Manfred Heller, Julius Rabl, Pavel Afanasyev et al. · 2022 · Nucleic Acids Research
3. The survivor strain: isolation and characterization of Phormidium yuhuli AB48, a filamentous phototactic cyanobacterium with biotechnological potential
   Moritz Koch, Avery J. C. Noonan, Yilin Qiu, Kalen Dofher, Brandon Kieft, Soheyl Mottahedeh, Manisha Shastri, Steven Hallam · 2022 · Frontiers in Bioengineering and Biotechnology
4. Shotgun Proteomics Analysis of Saliva and Salivary Gland Tissue from the Common Octopus Octopus vulgaris
   Legana C H W Fingerhut, Jan M. Strugnell, Pierre Faou, Álvaro Roura, Jia Zhang, Ira Cooke · 2018 · Journal of Proteome Research
5. In situ transformation of ethoxylate and glycol surfactants by shale-colonizing microorganisms during hydraulic fracturing
   Morgan V. Evans, Gordon J. Getzinger, Jenna L. Luek, Andrea J. Hanson, Molly McLaughlin, Jens Blotevogel, Susan A. Welch, Carrie Nicora, Samuel Owen Purvine, Chengdong Xu et al. · 2019 · The ISME Journal
6. Tailor: A Nonparametric and Rapid Score Calibration Method for Database Search-Based Peptide Identification in Shotgun Proteomics
   Pavel Sulimov, Attila Kertész‐Farkas · 2020 · Journal of Proteome Research
7. CIRFESS: An Interactive Resource for Querying the Set of Theoretically Detectable Peptides for Cell Surface and Extracellular Enrichment Proteomic Studies
   Matthew Waas, Jack Littrell, Rebekah L. Gundry · 2020 · Journal of the American Society for Mass Spectrometry
8. PASS-DIA: A Data-Independent Acquisition Approach for Discovery Studies
   Dong‐Gi Mun, Santosh Renuse, Mayank Saraswat, Anil Kumar Madugundu, Savita Udainiya, Hokeun Kim, Sung Kyu Robin Park, Hui Zhao, Raja Sekhar Nirujogi, Chan Hyun Na et al. · 2020 · Analytical Chemistry
9. The Exposed Proteomes of Brachyspira hyodysenteriae and B. pilosicoli
   Vanessa Casas, Santiago Vadillo, Carlos San Juan, Montserrat Carrascal, Joaquín Abián · 2016 · Frontiers in Microbiology
10. An antisense RNA capable of modulating the expression of the tumor suppressor microRNA-34a
    Jason T. Serviss, Nathanael Andrews, Jimmy Van den Eynden, Felix Clemens Richter, Miranda Houtman, Mattias Vesterlund, Laura Schwarzmueller, Per Johnsson, Erik Larsson, Dan Grandér et al. · 2018 · Cell Death and Disease
11. Proteomics Goes to Court: A Statistical Foundation for Forensic Toxin/Organism Identification Using Bottom-Up Proteomics
    Kristin H. Jarman, Natalie C. Heller, Sarah C. Jenson, Janine R. Hutchison, Brooke L. Deatherage Kaiser, Samuel Payne, David S. Wunschel, Eric D. Merkley · 2018 · Journal of Proteome Research
12. Editing of the Proteolytic System of Lactococcus lactis Increases Its Bioactive Potential
    Chenxi Huang, Jan Kok · 2020 · Applied and Environmental Microbiology
13. Silencing of Opisthorchis viverrini Tetraspanin Gene Expression Results in Reduced Secretion of Extracellular Vesicles
    Sujittra Chaiyadet, Javier Sotillo, Watchara Krueajampa, Sophita Thongsen, Michael J. Smout, Paul J. Brindley, Thewarach Laha, Alex C. Loukas · 2022 · Frontiers in Cellular and Infection Microbiology
14. Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts
    Samuel T. Coradetti, Paul Adamczyk, Di Liu, Yuqian Gao, Peter B. Otoupal, Gina M. Geiselman, Bobbie‐Jo Webb‐Robertson, Meagan Burnet, Young‐Mo Kim, Kristin Burnum-Johnson et al. · 2023 · Microbial Cell Factories
15. Remodeling of the human skeletal muscle proteome found after long-term endurance training but not after strength training
    Eric B. Emanuelsson, Muhammad Arif, Stefan Markus Reitzner, Sean Perez, Maléne E. Lindholm, Adil Mardinoğlu, Carsten O. Daub, Carl Johan Sundberg, Mark A. Chapman · 2023 · iScience
16. Bidirectional de novo peptide sequencing using a transformer model
    Sangjeong Lee, Hyunwoo Kim · 2024 · PLoS Computational Biology
17. Uncertainty estimation of predictions of peptides’ chromatographic retention times in shotgun proteomics
    Heydar Maboudi Afkham, Xuanbin Qiu, Matthew The, Lukas Käll · 2016 · Bioinformatics
18. Methods to Calculate Spectrum Similarity
    Şule Yılmaz, Elien Vandermarliere, Lennart Martens · 2016 · Methods in molecular biology
19. Proteomics Coupled with Metabolite and Cell Wall Profiling Reveal Metabolic Processes of a Developing Rice Stem Internode
    Fan Lin, Brad J. Williams, Padmavathi A. V. Thangella, Adam Ladak, Athena Schepmoes, Hernando J. Olivos, Kangmei Zhao, Stephen Callister, Laura Bartley · 2017 · Frontiers in Plant Science
20. Proteomic Analysis of Combined Gemcitabine and Birinapant in Pancreatic Cancer Cells
    Xu Zhu, Xiaomeng Shen, Jun Qu, Robert M. Straubinger, William J. Jusko · 2018 · Frontiers in Pharmacology
21. A simple dual online ultra-high pressure liquid chromatography system (sDO-UHPLC) for high throughput proteome analysis
    Hangyeore Lee, Dong‐Gi Mun, Jingi Bae, Hokeun Kim, Se Yeon Oh, Young Soo Park, Jae-Hyuk Lee, Sang‐Won Lee · 2015 · The Analyst
22. Integrative Multi-PTM Proteomics Reveals Dynamic Global, Redox, Phosphorylation, and Acetylation Regulation in Cytokine-Treated Pancreatic Beta Cells
    Austin Gluth, Xiaolu Li, Marina A. Gritsenko, Matthew J. Gaffrey, Doo Nam Kim, Priscila M. Lalli, Rosalie Chu, Nicholas J. Day, Tyler J. Sagendorf, Matthew E Monroe et al. · 2024 · Molecular & Cellular Proteomics
23. Open-Source and FAIR Research Software for Proteomics
    Yasset Pérez‐Riverol, Wout Bittremieux, William Stafford Noble, Lennart Martens, Aivett Bilbao Pena, Michael R. Lazear, Björn Andreas Grüning, Daniel S. Katz, Michael J. MacCoss, Chengxin Dai et al. · 2025 · Journal of Proteome Research
24. Improved 6-Plex Tandem Mass Tags Quantification Throughput Using a Linear Ion Trap–High-Energy Collision Induced Dissociation MS3 Scan
    Jane M. Liu, Michael J. Sweredoski, Sonja Y. Hess · 2016 · Analytical Chemistry
25. Combining High-Resolution and Exact Calibration To Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution MS2 Data
    Andy Lin, James Jeffry Howbert, William Stafford Noble · 2018 · Journal of Proteome Research
26. gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms
    Maria Muñoz-Benavent, Felix Hartkopf, Tim Van Den Bossche, Vitor C. Piro, Carlos García‐Ferris, Amparo Latorre, Bernhard Y. Renard, Thilo Muth · 2020 · NAR Genomics and Bioinformatics
27. Comparison of different digestion methods for proteomic analysis of isolated cells and FFPE tissue samples
    Artur Piróg, Jakub Faktor, Zuzanna Urban‐Wójciuk, Sachin Kote, Elżbieta Chruściel, Łukasz Arcimowicz, Natalia Maria Marek-Trzonkowska, Borek Vojtesek, Ted R. Hupp, Sofian Al Shboul et al. · 2021 · Talanta
28. Unified and Standardized Mass Spectrometry Data Processing in Python Using spectrum_utils
    Wout Bittremieux, Lev I. Levitsky, Matteo Pilz, Timo T. Sachsenberg, Florian Huber, Mingxun Wang, Pieter C. Dorrestein · 2023 · Journal of Proteome Research
29. Challenges and Opportunities for Single-cell Computational Proteomics
    Hannah Boekweg, Samuel Payne · 2023 · Molecular & Cellular Proteomics
30. Viral proteogenomic and expression profiling during productive replication of a skin-tropic herpesvirus in the natural host
    Jeremy D. Volkening, Stephen J. Spatz, Nagendraprabhu Ponnuraj, Haji Akbar, Justine V. Arrington, Widaliz Vega‐Rodriguez, Keith William Jarosinski · 2023 · PLoS Pathogens
31. Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry
    Katherine Naasko, D. V. Naylor, Emily B. Graham, Sneha Couvillion, Robert Danczak, Nikola Tolić, Carrie Nicora, Steven C. Fransen, Haiying Tao, Kirsten Hofmockel et al. · 2023 · mBio
32. Machine Learning Strategies to Tackle Data Challenges in Mass Spectrometry-Based Proteomics
    Ceder Dens, Charlotte Adams, Kris Laukens, Wout Bittremieux · 2024 · Journal of the American Society for Mass Spectrometry
33. Proteogenomics: Key Driver for Clinical Discovery and Personalized Medicine
    Ruggero Barbieri, Victor Guryev, Corry‐Anke Brandsma, Frank Suits, Rainer Bischoff, Peter L. Horvatovich · 2016 · Advances in experimental medicine and biology
34. A Strong Neutrophil Elastase Proteolytic Fingerprint Marks the Carcinoma Tumor Proteome
    Michał Kistowski, Janusz Dȩbski, Jakub Karczmarski, Agnieszka Paziewska, Jacek Olędzki, Michał Mikuła, Jerzy Ostrowski, Michał Dadlez · 2016 · Molecular & Cellular Proteomics
35. Relative protein quantification and accessible biology in lung tumor proteomes from four LC‐MS/MS discovery platforms
    Paul A. Stewart, Bin Fang, Robbert J.C. Slebos, Guolin Zhang, Adam L. Borne, Katherine M. Fellows, Jamie K. Teer, Y. Ann Chen, Eric A. Welsh, Steven A. Eschrich et al. · 2017 · PROTEOMICS
36. Improvements in Mass Spectrometry Assay Library Generation for Targeted Proteomics
    Johan Teleman, Simon Hauri, Johan A. Malmström · 2017 · Journal of Proteome Research
37. Proteome and transcriptome profiling of equine myofibrillar myopathy identifies diminished peroxiredoxin 6 and altered cysteine metabolic pathways
    Stephanie J. Valberg, Sudeep Perumbakkam, Erica C. McKenzie, Carrie J. Finno · 2018 · Physiological Genomics
38. Fast Proteome Identification and Quantification from Data-Dependent Acquisition–Tandem Mass Spectrometry (DDA MS/MS) Using Free Software Tools
    Jesse G. Meyer · 2019 · Methods and Protocols
39. Small-molecule inhibitor of HlyU attenuates virulence of Vibrio species
    Zee-Won Lee, Byoung Sik Kim, Kyung Ku Jang, Ye‐Ji Bang, Suhyeon Kim, Nam‐Chul Ha, Young Hyun Jung, Hyun Jik Lee, Ho Jae Han, Jong‐Seo Kim et al. · 2019 · Scientific Reports
40. Benzo[a]pyrene Induction of Glutathione S-Transferases: An Activity-Based Protein Profiling Investigation
    Ethan G. Stoddard, Bryan Killinger, Subhasree Ashok Nag, Jude Martin, RICHARD A. CORLEY, Jordan Ned Smith, Aaron Wright · 2019 · Chemical Research in Toxicology
41. Identification and quantification of sites of nitration and oxidation in the key matrix protein laminin and the structural consequences of these modifications
    Lasse G. Lorentzen, Christine Y. Chuang, Adelina Rogowska-Wrzesińska, Michael J. Davies · 2019 · Redox Biology
42. An integrated transcriptomic- and proteomic-based approach to evaluate the human skin sensitization potential of glyphosate and its commercial agrochemical formulations
    Tim Lindberg, Renato Ivan de Ávila, Kathrin Stephanie Zeller, Fredrik Levander, Dennis Eriksson, Aakash Chawade, Malin Lindstedt · 2020 · Journal of Proteomics
43. The Campylobacter jejuni CiaD effector co-opts the host cell protein IQGAP1 to promote cell entry
    Nicholas M. Negretti, Christopher R. Gourley, Prabhat Kumar Talukdar, Gérémy Clair, Courtney M. Klappenbach, Cody J. Lauritsen, Joshua Adkins, Michael E. Konkel · 2021 · Nature Communications
44. Opposing roles of p38α-mediated phosphorylation and PRMT1-mediated arginine methylation in driving TDP-43 proteinopathy
    Mari Aikio, Hana M. Odeh, Heike J. Wobst, Bo Lim Lee, Úna Chan, Jocelyn C. Mauna, Korrie L. Mack, Bradley Class, Thomas A. Ollerhead, Alice Flynn Ford et al. · 2025 · Cell Reports
45. A Triple Knockout Isobaric-Labeling Quality Control Platform with an Integrated Online Database Search
    Jeremy P. Gygi, Ramin Rad, José Navarrete-Perea, Simon Younesi, Steven P. Gygi, João A. Paulo · 2020 · Journal of the American Society for Mass Spectrometry
46. Transcriptome and Proteome Analysis in LUHMES Cells Overexpressing Alpha-Synuclein
    Matthias Höllerhage, Markus Stepath, Michael Kohl, Kathy Pfeiffer, Oscar Wing Ho Chua, Linghan Duan, Franziska Hopfner, Martin Eisenacher, Katrin Marcus, Günter U. Höglinger · 2022 · Frontiers in Neurology
47. The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides
    Georges Bedran, Hans-Christof Gasser, Kenneth Weke, Tongjie Wang, Dominika Bedran, Alexander Laird, Christophe Battail, Fabio Massimo Zanzotto, Cátia Pesquita, Håkan Axelson et al. · 2023 · Cancer Immunology Research
48. Identification of Small Novel Coding Sequences, a Proteogenomics Endeavor
    Volodimir Olexiouk, Gerben Menschaert · 2016 · Advances in experimental medicine and biology
49. Dinitrogenase-Driven Photobiological Hydrogen Production Combats Oxidative Stress in Cyanothece sp. Strain ATCC 51142
    Natalie Sadler, Hans Christopher Bernstein, Matthew R. Melnicki, Moiz A. Charania, Eric Allen Hill, Lindsey N. Anderson, Matthew E Monroe, Richard D. Smith, Alexander S. Beliaev, Aaron Wright · 2016 · Applied and Environmental Microbiology
50. Proteogenomic Investigation of Strain Variation in Clinical Mycobacterium tuberculosis Isolates
    Tiaan D. J. Heunis, Anzaan Dippenaar, Robin M. Warren, Paul D. van Helden, Ruben Gerhard van der Merwe, Nicolaas C. Gey van Pittius, Arnab Pain, Samantha Leigh Sampson, David L. Tabb · 2017 · Journal of Proteome Research
51. Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues
    Jianying Zhou, Lijun Chen, Bai Zhang, Yuan Tian, Tao Liu, Stefani N. Thomas, Li Chen, Michael Schnaubelt, Emily S. Boja, Tara Hiltke et al. · 2017 · Journal of Proteome Research
52. Integration of Proteomics and Metabolomics Into the Design, Build, Test, Learn Cycle to Improve 3-Hydroxypropionic Acid Production in Aspergillus pseudoterreus
    Kyle Pomraning, Ziyu Dai, Nathalie Munoz Munoz, Young‐Mo Kim, Yuqian Gao, Shuang Hui Deng, Joonhoon Kim, Beth A. Hofstad, Marie Swita, Teresa Lemmon et al. · 2021 · Frontiers in Bioengineering and Biotechnology
53. Ion Mobility Coupled to a Time-of-Flight Mass Analyzer Combined With Fragment Intensity Predictions Improves Identification of Classical Bioactive Peptides and Small Open Reading Frame-Encoded Peptides
    Marlies K. R. Peeters, Geert Baggerman, Ralf Gabriels, Elise Pepermans, Gerben Menschaert, Kurt Boonen · 2021 · Frontiers in Cell and Developmental Biology
54. Efficient Exploitation of Separation Space in Two-Dimensional Liquid Chromatography System for Comprehensive and Efficient Proteomic Analyses
    Hangyeore Lee, Dong‐Gi Mun, Jeong Eun So, Jingi Bae, Hokeun Kim, Christophe Masselon, Sang‐Won Lee · 2016 · Analytical Chemistry
55. The impact of noise and missing fragmentation cleavages on de novo peptide identification algorithms
    Kevin Mcdonnell, Enda Howley, Florence Abram · 2022 · Computational and Structural Biotechnology Journal
56. Statistical Analysis of Post-Translational Modifications Quantified by Label-Free Proteomics Across Multiple Biological Conditions with R: Illustration from SARS-CoV-2 Infected Cells
    Quentin Giai Gianetto · 2021 · Methods in molecular biology
57. Forecasting the dynamics of a complex microbial community using integrated meta-omics
    Francesco Delogu, Benoit Josef Kunath, Pedro Queirós, Rashi Halder, Laura Lebrun, Phillip Byron Pope, Patrick May, Stefanie Widder A, Emilie E. L. Muller, Paul Wilmes · 2023 · Nature Ecology & Evolution
58. Dynamic nitrogen fixation in an aerobic endophyte of Populus
    Andrew W. Sher, Jayde A. Aufrecht, Daisy Herrera, Amy Zimmerman, Young‐Mo Kim, Nathalie Munoz Munoz, Jesse B. Trejo, Vanessa Paurus, John Cliff, Dehong Hu et al. · 2024 · The ISME Journal
59. A secretome profile indicative of oleate-induced proliferation of HepG2 hepatocellular carcinoma cells
    Soyeon Park, Ji-Hwan Park, Heejung Jung, Jin‐Hyeok Jang, Sang Hyun Ahn, Younah Kim, Pann‐Ghill Suh, Sehyun Chae, Jong Hyuk Yoon, Sung Ho Ryu et al. · 2018 · Experimental & Molecular Medicine
60. A Comprehensive Evaluation of MS/MS Spectrum Prediction Tools for Shotgun Proteomics
    Rui Xu, Jie Sheng, Mingze Bai, Kunxian Shu, Yunping Zhu, Cheng Chang · 2020 · PROTEOMICS
61. Deep learning embedder method and tool for mass spectra similarity search
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62. High-Resolution Proteomic Profiling Shows Sexual Dimorphism in Zebrafish Heart-Associated Proteins
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63. Platforms and Pipelines for Proteomics Data Analysis and Management
    Marius Cosmin Codrea, Sven Nahnsen · 2016 · Advances in experimental medicine and biology
64. Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom
    J. Scott P. McCain, Andrew Ellis Allen, Erin M. Bertrand · 2021 · The ISME Journal
65. DDASSQ: An open‐source, multiple peptide sequencing strategy for label free quantification based on an OpenMS pipeline in the KNIME analytics platform
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66. MS-PyCloud: A Cloud Computing-Based Pipeline for Proteomic and Glycoproteomic Data Analyses
    Yingwei Hu, Michael Schnaubelt, Li Chen, Bai Zhang, Trung Hoàng, T. Mamie Lih, Zhen Zhang, Hui Zhang · 2024 · Analytical Chemistry
67. Efficient Microscale Basic Reverse Phase Peptide Fractionation for Global and Targeted Proteomics
    Hyoungjoo Lee, Hye‐Jung Kim, Daniel C. Liebler · 2016 · Journal of Proteome Research
68. ProteinExplorer: A Repository-Scale Resource for Exploration of Protein Detection in Public Mass Spectrometry Data Sets
    Benjamin S Pullman, Julie Wertz, Jeremy Carver, Nuno Bandeira · 2018 · Journal of Proteome Research
69. Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability*
    Kuan-lin Huang, Yige Wu, Tina M. Primeau, Yi-Ting Wang, Yuqian Gao, Joshua F. McMichael, Adam David Scott, Song Cao, Michael C. Wendl, Kimberly J. Johnson et al. · 2019 · Molecular & Cellular Proteomics
70. TaxIt: An Iterative Computational Pipeline for Untargeted Strain-Level Identification Using MS/MS Spectra from Pathogenic Single-Organism Samples
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71. Increased CSF Levels of Apolipoproteins and Complement Factors in Trigeminal Neuralgia Patients–In Depth Proteomic Analysis Using Mass Spectrometry
    Sami Abu Hamdeh, Payam Emami Khoonsari, Ganna Shevchenko, Torsten Gordh, Hans Ericson, Kim Kultima · 2020 · Journal of Pain
72. Re-routing of Sugar Catabolism Provides a Better Insight Into Fungal Flexibility in Using Plant Biomass-Derived Monomers as Substrates
    Tania Chroumpi, Mao Peng, Lye Meng Markillie, Hugh D. Mitchell, Carrie Nicora, Chelsea M. Hutchinson, Vanessa Paurus, Nikola Tolić, Chaevien S. Clendinen, Galya Orr et al. · 2021 · Frontiers in Bioengineering and Biotechnology
73. High performance computing framework for tera-scale database search of mass spectrometry data
    Muhammad Haseeb, Fahad Saeed · 2021 · Nature Computational Science
74. Scribe: Next Generation Library Searching for DDA Experiments
    Brian C. Searle, Ariana E. Shannon, Damien B. Wilburn · 2023 · Journal of Proteome Research
75. ArtA-Dependent Processing of a Tat Substrate Containing a Conserved Tripartite Structure That Is Not Localized at the C Terminus
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76. A Meta-proteogenomic Approach to Peptide Identification Incorporating Assembly Uncertainty and Genomic Variation
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77. Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements
    Shangzhong Li, Seong Won Cha, Kelly Heffner, Deniz Baycın Hızal, Michael A. Bowen, Raghothama Chaerkady, Robert Norman Cole, Vijay Tejwani, Prashant Kaushik, Michael A. Henry et al. · 2019 · Journal of Proteome Research
78. Target-small decoy search strategy for false discovery rate estimation
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79. Ozone-derived oxysterols impair lung macrophage phagocytosis via adduction of some phagocytosis receptors
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80. Novel Cyclic Peptides from Lethal Amanita Mushrooms through a Genome-Guided Approach
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81. PeptideShaker Online: A User-Friendly Web-Based Framework for the Identification of Mass Spectrometry-Based Proteomics Data
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82. Calibr improves spectral library search for spectrum-centric analysis of data independent acquisition proteomics
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83. Novel Diagnostic Biomarkers for High-Grade Serous Ovarian Cancer Uncovered by Data-Independent Acquisition Mass Spectrometry
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84. Comparison of Database Searching Programs for the Analysis of Single-Cell Proteomics Data
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85. Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine–Exocrine Signaling Sphere of Influence
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86. Short-term acidification promotes diverse iron acquisition and conservation mechanisms in upwelling-associated phytoplankton
    Robert H. Lampe, Tyler H. Coale, Kiefer Forsch, Loay J. Jabre, Samuel A. H. Kekuewa, Erin M. Bertrand, Aleš Horák, Miroslav Obornı́k, Ariel J. Rabines, Elden E. Rowland et al. · 2023 · Nature Communications
87. Challenges in the discovery of tumor-specific alternative splicing-derived cell-surface antigens in glioma
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88. Proteomic signatures of Alzheimer's disease and Lewy body dementias: A comparative analysis
    Anna Canal-García, Rui Mamede Branca, Paul T. Francis, Clive G. Ballard, Bengt G. Winblad, Janne Lehtiö, Per Nilsson, Dag Aarsland, Joana B. Pereira, Erika Bereczki · 2024 · Alzheimer s & Dementia
89. Synergism of proteomics and mRNA sequencing for enzyme discovery
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90. microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network
    Yan Zhou, Oliver Frings, Rui Mamede Branca, Jorrit Boekel, Carlos le Sage, Erik Fredlund, Reuven Agami, Lukas M. Orre · 2016 · Oncogene
91. A Proteogenomic Resource Enabling Integrated Analysis of Listeria Genotype–Proteotype–Phenotype Relationships
    Adithi R. Varadarajan, Sandra Götze, Maria P. Pavlou, Virginie Grosboillot, Yang Shen, Martin J. Loessner, Christian H. Ahrens, Bernd Wollscheid · 2020 · Journal of Proteome Research
92. Functional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies Between Lineages of Wood-Degrading Fungi With Redundant Wood Decay Mechanisms
    Gerald N. Presley, Jiwei Zhang, Samuel Owen Purvine, Jonathan S. Schilling · 2020 · Frontiers in Microbiology
93. Multiplexed Post-Experimental Monoisotopic Mass Refinement (mPE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation
    Inamul Hasan Madar, Seung-Ik Ko, Hokeun Kim, Dong‐Gi Mun, Sangtae Kim, Richard D. Smith, Sang‐Won Lee · 2016 · Analytical Chemistry
94. Towards highly sensitive deep learning-based end-to-end database search for tandem mass spectrometry
    Yonghan Yu, Ming Li · 2025 · Nature Machine Intelligence
95. The Open Pediatric Cancer Project
    Zhuangzhuang Geng, Eric K. Wafula, Ryan J. Corbett, Yuanchao Zhang, Run Jin, Krutika Satish Gaonkar, Sangeeta Shukla, Komal S. Rathi, Dave Hill, Aditya Lahiri et al. · 2025 · GigaScience
96. Simple Method To Characterize the Ciliary Proteome of Multiciliated Cells
    Hyo Jung Sim, Seongmin Yun, Ha Eun Kim, Keun Yeong Kwon, Gun‐Hwa Kim, Sung‐Ho Yun, Byung Gyu Kim, Kyungjae Myung, Tae Joo Park, Taejoon Kwon · 2019 · Journal of Proteome Research
97. HyperSpec: Ultrafast Mass Spectra Clustering in Hyperdimensional Space
    Weihong Xu, Jaeyoung Kang, Wout Bittremieux, Niema Moshiri, Tajana Rosing · 2023 · Journal of Proteome Research
98. Machine learning‐based peptide‐spectrum match rescoring opens up the immunopeptidome
    Charlotte Adams, Kris Laukens, Wout Bittremieux, Kurt Boonen · 2023 · PROTEOMICS
99. Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures
    Mak A. Saito, Jaclyn K. Saunders, Matthew R. McIlvin, Erin M. Bertrand, J. A. Breier, Margaret Mars Brisbin, Sophie M. Colston, Jaimee R. Compton, Timothy J. Griffin, W. Judson Hervey et al. · 2024 · Biogeosciences
100. Proteogenomic characterization of molecular and cellular targets for treatment-resistant subtypes in locally advanced cervical cancers
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