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

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Items 901–999 of 999

1. DiNovo enables high-coverage and high-confidence de novo peptide sequencing via mirror proteases and deep learning
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2. A Framework for Database Search with AI Models in Mass Spectrometry-Based Proteomics
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3. Harnessing toxin-mediated ribosome stalling as a complementary tool to annotate bacterial ORFs
   Eduardo Artur Troian, Valdir C. Barth, Unnati Chauhan, Haiyan Zheng, Caifeng Zhao, Jumei Zeng, Robert N. Husson, Nancy A. Woychik · 2026 · Nucleic Acids Research
4. BioProEV: A Bioinformatics Pipeline for Biologically‐Relevant Handling of Missing Values in the Analysis of Extracellular Vesicles by Mass Spectrometry
   Pâmella Miranda, Jose Marchan, Annemarijn Offens, Ruihan Zhou, Mathieu Y. Brunet, Loes Teeuwen, Maria Eldh, Susanne Gabrielsson, Phillip T. Newton · 2026 · Journal of Extracellular Biology
5. Tesorai Search: Cloud-based Database Search Engine Boosts Identifications for Mass Spectrometry Proteomics With a Pretrained Peptide-spectrum Deep-learning Model
   Maximilien Burq, Dejan Štepec, Juan Restrepo, Jure Žbontar, Shamil Z. Urazbakhtin, Bryan Crampton, Rehan Chinoy, Melissa Miao, Jüergen Cox, Peter Cimermančič · 2026 · Journal of Molecular Biology
6. Faster and more accurate graphical model identification of tandem mass spectra using trellises
   Shengjie Wang, John T. Halloran, Jeff Bilmes, William Stafford Noble · 2016 · Bioinformatics
7. Bioinformatics for Mass Spectrometry-Based Proteomics
   Rebekah L. Gundry · 2016 · Springer eBooks
8. MS2-Based Quantitation
   Marc Vaudel · 2016 · Royal Society of Chemistry eBooks
9. Real-time laser induced chemical derivatizations of peptide N-Terminus for in-situ mass spectrometric sequencing at sub-picomole and nanosecond scale
   Juan Zhang, Shanshan Jia, Wen‐Ting Lu, Weidan Li, Ruowei Jiang, Yanping Liu, Xiaojie Yang, Si Zou, Xuekun Zou, Hongying Zhong · 2019 · Analytica Chimica Acta
10. Understanding the Limit of Open Search in the Identification of Peptides With Post-translational Modifications — A Simulation-Based Study
    Jiaan Dai, Fengchao Yu, Ning Li, Weichuan Yu · 2020 · IEEE Transactions on Computational Biology and Bioinformatics
11. PRiSM: A prototype for exhaustive, restriction‐free database searching for mass spectrometry–based identification
    Joris Van Houtven, Kurt Boonen, Geert Baggerman, Manor Askenazi, Kris Laukens, Jef Hooyberghs, Dirk Valkenborg · 2020 · Rapid Communications in Mass Spectrometry
12. FPTMS: Frequency-based approach to identify the peptide from the low-energy collision-induced dissociation tandem mass spectra
    Sangeetha Ramachandran, Tessamma Thomas · 2021 · Journal of Proteomics
13. The potential for using shell proteins in gastropod systematics, assessed in patellogastropod limpets
    Donald James Colgan · 2021 · Zoological Journal of the Linnean Society
14. Application of Top-Down Deconvolution Tools to Bottom-Up Mass Spectrometry Data: Advantages and Limitations
    Kirill Tyshuk, Kira Vyatkina · 2022 · Springer proceedings in physics
15. A DISTRIBUTED ALGORITHM FOR PROTEIN IDENTIFICATION FROM TANDEM MASS SPECTROMETRY DATA
    Katarzyna ORZECHOWSKA, Tymon Rubel, Robert Kurjata, Krzysztof Zaremba · 2022 · Applied Computer Science
16. Exact p‐value calculation for XCorr scoring of high‐resolution MS/MS data
    Kishankumar Bhimani, Arina Peresadina, Dmitrii Vozniuk, Attila Kertész‐Farkas · 2023 · PROTEOMICS
17. Untargeted, tandem mass spectrometry metaproteome of Columbia River sediments
    Josué A. Rodríguez-Ramos, Carrie Nicora, Samuel Owen Purvine, Mikayla Borton, Bridget B. McGivern, David W Hoyt, Mary S. Weir Lipton, Kelly C. Wrighton · 2024 · Microbiology Resource Announcements
18. Identification of Novel Bacterial Microproteins Encoded by Small Open Reading Frames Using a Computational Proteogenomics Workflow
    Eduardo Vieira de Souza, Cristiano Valim Bizarro · 2024 · Methods in molecular biology
19. Analysis and Interpretation of Pharmacoproteomic Data
    Nihali Jain, Parixit Prajapati, Vipul D. Prajapati, Aishwariya Patel, Hemal Tandel, Jayvadan K. Patel · 2024 · Springer eBooks
20. A Multi-Omic Phenobank Reveals Axes of Glioblastoma Growth, Invasion, and Therapeutic Vulnerability
    Cecilia C. Krona, Soumi Kundu, Emil Rosén, Filippa Kruse, Madeleine Skeppås, Haris Babačić, Ida Larsson, Ludmila Elfineh, Maya Jeje Schuan Lü, Maria Escriva Conde et al. · 2026 · Neuro-Oncology
21. Distinguishing N-Terminal Methylation from Near-Isobaric Modifications by Statistical Analysis of Mass Error Distributions of Fragment Ions
    Hankyul Lee, Shinyeong Ju, Seonjeong Lee, So Ha Lee, Sang‐Yoon Kim, Narae Park, Cheol-Sang Hwang, Kang-Sik Park, Cheolju Lee · 2025 · Journal of Proteome Research
22. An Integral Activity-Based Protein Profiling Method for Higher Throughput Determination of Protein Target Sensitivity to Small Molecules
    Chathuri Jeewanthi Kombala Nanayakkara Thambiliya, Agne Sveistyte, Tong Zhang, Leo J. Gorham, Gerard X. Lomas, John Melchior, Priscila M. Lalli, Vanessa Paurus, Stephen Callister, Aaron Wright et al. · 2025 · ACS Chemical Biology
23. Quantitative Analysis of Mass Spectrometry-Based Proteomics Data
    Thang V. Pham, Connie R. Jiménez · 2019 · Neuromethods
24. ForestDSH: a universal hash design for discrete probability distributions
    Arash Gholami Davoodi, Sean Chang, Hyun Gon Yoo, Anubhav Baweja, Mihir Mongia, Hosein Mohimani · 2021 · Data Mining and Knowledge Discovery
25. Validation of Chimeric Fusion Peptides Using Proteomics Data
    Sandeep Singh, Hui Li · 2019 · Methods in molecular biology
26. A Protein Identification Algorithm Optimization for Mass Spectrometry Data using Deep Learning
    Rui Xu, Mingze Bai, Kunxian Shu, Yilong Liang, Yunping Zhu, Cheng Chang · 2020 · International Conference on Advanced Electronic Materials, Computers and Software Engineering (AEMCSE)
27. Utility of the “omics” in kidney disease: Methods of analysis, sampling considerations, and technical approaches in renal biomarkers
    Vanessa Moreno · 2020 · Elsevier eBooks
28. A rapid response vaccine development strategy for newcastle disease in poultry
    SR Maremagae, Cornelius Carlos Bezuidenhout, AM Murphy, Michael A. Jarvis, Preneshni R. Naicker, PJ Lebea · 2020 · African Journal of Food Agriculture Nutrition and Development
29. Analysis of Label-Based Quantitative Proteomics Data Using IsoProt
    Johannes Griss, Veit Schwämmle · 2021 · Methods in molecular biology
30. A complete search of combinatorial peptide library greatly benefited from probabilistic incorporation of prior knowledge
    Miroslav Hruska, Dušan Holub · 2021 · International Journal of Mass Spectrometry
31. Effect of polyethylene glycol 20 000 on protein extraction efficiency of formalin-fixed paraffin-embedded tissues in South Africa
    Sophia Catherine Rossouw, Hocine Bendou, Liam Bell, Jonathan Rigby, Alan Gilbert Christoffels · 2021 · African Journal of Laboratory Medicine
32. Multiaspect Examinations of Possible Alternative Mappings of Identified Variant Peptides: A Case Study on the HEK293 Cell Line
    Wai-Kok Choong, Ting‐Yi Sung · 2022 · ACS Omega
33. Anais da XXV Semana de Biomedicina
    2019
34. A novel framework to quantify uncertainty in peptide-tandem mass spectrum matches with application to nanobody peptide identification
    Chris G. McKennan, Zhe Sang, Yi Shi · 2025 · The Annals of Applied Statistics
35. Stokab Helps Build a Smarter Stockholm
    Benoot Felten · 2015 · SSRN Electronic Journal
36. Shifting the Paradigm: Peptide-Centric Analysis of Systematically Sampled Mass Spectrometry Data
    Ying Sonia Ting · 2016 · ResearchWorks at the University of Washington (University of Washington)
37. DDIA: data dependent-independent acquisition proteomics - DDA and DIA in a single LC-MS/MS run
    Shenheng Guan, Paul P. Taylor, Ziwei Han, Michael F. Moran, Bin Ma · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
38. A generalizable method for false-discovery rate estimation in mass spectrometry-based lipidomics
    Grant M. Fujimoto, Jennifer E Kyle, Joon‐Yong Lee, Thomas Metz, Samuel Payne · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
39. Evolutionary Algorithms for Improving De Novo Peptide Sequencing
    Samaneh Azari · 2020
40. Transposable Element-Gene Splicing Modulates the Transcriptional Landscape of Human Pluripotent Stem Cells
    Isaac A. Babarinde, Gang Ma, Yuhao Li, Boping Deng, Zhiwei Luo, Hao Liu, Mazid Md. Abdul, Carl Ward, Minchun Chen, Xiuling Fu et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
41. Direct mapping of Peptide-to-Spectra-Matches to genome information facilitates qualifying proteomics information
    John C. Anders, Hannes Petruschke, Nico Jehmlich, Sven‐Bastiaan Haange, Martin von Bergen�, Peter Florian Stadler · 2021 · Research Square
42. Proteomic Dissection of a Giant Cell
    Athena W. Lin, Paul Piehowski, Chia‐Feng Tsai, Tatyana Makushok, Lian Yi, Ulises Diaz, Connie H. Yan, Diana Summers, Pranidhi Sood, Richard D. Smith et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
43. Forecasting of a complex microbial community using 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 · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
44. Mass spectrometry-based proteomic analysis of PDAC samples
    Do Young Hyeon, Dowoon Nam, Youngmin Han, Duk Ki Kim, Gibeom Kim, Daeun Kim, Jingi Bae, Seunghoon Back, Dong‐Gi Mun, Inamul Hasan Madar et al. · 2023 · Research Square
45. IQMMA: an efficient MS1 intensity extraction using multiple feature detection algorithms for DDA proteomics
    Valeriy I. Postoenko, Leyla A. Garibova, Lev I. Levitsky, Julia A. Bubis, Mikhail V. Gorshkov, Mark V. Ivanov · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
46. Whitefly effector G4 interacts with tomato proteins of which MIPDB141 affects whitefly performance
    Diana Naalden, Wannes Dermauw, Aris Ilias, Geert Baggerman, Marieke Mastop, Sarmina Dangol, Nicolas Frédéric Gaertner, Winfried Roseboom, Mark A. C. J. Kwaaitaal, Gertjan Kramer et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
47. Regulation of bacterial stringent response by an evolutionary conserved ribosomal protein L11 methylation
    Hanna E. Walukiewicz, Yuliya Farris, Meagan Burnet, Sarah C. Feid, Youngki You, David G. Christensen, Samuel H. Payne, Alan J. Wolfe, Christopher V. Rao, Ernesto Satoshi Nakayasu · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
48. GroEL-proteotyping of bacterial communities by tandem mass spectrometry
    Simon Klaes, Shobhit Madan, Darja Deobald, Myriel Cooper, Lorenz Adrian · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
49. π -PrimeNovo: An Accurate and Efficient Non-Autoregressive Deep Learning Model for De Novo Peptide Sequencing
    Xiang Zhang, Tianze Ling, Zhi Xiang Jin, Sheng Xu, Zhiqiang Gao, Boyan Sun, Zijie Qiu, Nanqing Dong, Guangshuai Wang, Guibin Wang et al. · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
50. Elemental allocation to molecular drivers of biogeochemistry in the Southern Ocean
    Loay J. Jabre, Elden E. Rowland, Charlotte Eich, Mathijs van Manen, Corina P. D. Brussaard, Rob Middag, Erin M. Bertrand · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
51. DelPi Learns Generalizable Peptide–Signal Correspondence for Mass Spectrometry-Based Proteomics
    Jungkap Park, KyungGon Kim, Un‐Beom Kang, Sangtae Kim · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
52. New developments in high-resolution mass spectrometry for proteomic analysis applied to cultural heritage : study of intact proteins, their cross-linking and interaction in artworks and museum objects
    Francesca Galluzzi · 2021 · theses.fr (ABES)
53. Computational methods and graphical models for integrative proteogenomics
    Franziska Zickmann · 2015 · Universitätsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver
54. Deconvolution of immunome and degradome repertoires using computational proteomics
    Stefano R. Bonissone · 2015 · eScholarship (California Digital Library)
55. The Application of Hydrogen/Deuterium Exchange and Covalent Labeling Coupled with Mass Spectrometry to Examine Protein Structure
    Nicholas B. Borotto · 2021 · ScholarWorks@UMassAmherst (University of Massachusetts Amherst)
56. FOCUS: MASS SPECTROMETRY-BASED STRATEGIES FOR NEUROPROTEOMICS AND PEPTIDOMICS: RESEARCH ARTICLE An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics
    Chaochao Wu, Matthew E Monroe, Zhe Xu, Gordon Slysz, Samuel Payne, Karin Rodland, Tao Liu, Richard D. Smith · 2015
57. Application of liquid chromatography-mass spectrometry-based protein and proteomic analytical approaches to chinese hamster ovary cell based industrial biopharmaceutical production
    Yuanwei Gao · 2016 · Digital Repository Service (Northeastern University)
58. Whole-genome analysis of Mycobacterium tuberculosis persister genes and investigation of the anti-tubercular compound lassomycin
    Lauren E Fitch · 2015 · Digital Repository Service (Northeastern University)
59. Enhancement of LC-MS proteomic analysis through novel data acquisition strategies
    Simion D. Kreimer · 2016 · Digital Repository Service (Northeastern University)
60. Mass Spectrometric Characterization of Recombinant Proteins
    Corey E. Bakalarski, Wendy N. Sandoval, Jennie Rebecca Lill · 2017 · Wiley eBooks
61. Bioinformatics Support for Farm Animal Proteomics
    Aivett Bilbao Pena, Frédérique Lisacek · 2018 · Springer eBooks
62. Onco-proteogenomic exploration of variant peptide detection in disease models and clinical specimens
    Lampros Dimitrakopoulos · 2017 · TSpace (University of Toronto)
63. Bioinformatic and Experimental Approaches for Deeper Metaproteomic Characterization of Complex Environmental Samples
    Ramsunder Iyer · 2017
64. Computational Framework for Data-Independent Acquisition Proteomics.
    Chih‐Chiang Tsou · 2016 · Deep Blue (University of Michigan)
65. Detecting Protein Variants within Mass Spectrometry Datasets
    Javier A. Alfaro · 2018 · TSpace (University of Toronto)
66. High-flow Nano-chromatography Columns Facilitate Rapid and High-quality Proteome Analysis on Standard Nano-LC Hardware
    Christopher S. Hughes, Hans H. Adomat, Stéphane LeBihan, Colin C. Collins, Poul H. B. Sorensen, Gregg B. Morin · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
67. Long noncoding RNAs are critical regulators of pancreatic islet development and function
    Ruth A. Singer · 2018
68. Mechanisms of decay and interspecific interactions of white and brown rot fungi
    Gerald N. Presley · 2018 · University of Minnesota Digital Conservancy (University of Minnesota)
69. BRAWNIN: A sORF-encoded Peptide Essential for Vertebrate Mitochondrial Complex III Assembly
    Shan Zhang, Chao Liang, Camille Mary, Baptiste Kerouanton, Joel Celio Francisco, Narendra Suhas Jagannathan, Volodimir Olexiouk, Jih Hou Peh, Claire Tang, Gio Fidelito et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
70. A Pre-computed Probabilistic Molecular Search Engine for Tandem Mass Spectrometry Proteomics
    Jeff Jones · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
71. Proteogenomics analysis of non-coding region encoded peptides in normal tissues and five cancer types
    Rong Xiang, Leyao Ma, Ming‐Yu Yang, Zetian Zheng, Xiaofang Chen, Fujian Jia, Fanfan Xie, Fuqiang Li, Kui Wu, Yafeng Zhu · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
72. Efficient Database Search via Tensor Distribution Bucketing
    Mihir Mongia, Benjamin Soudry, Arash Gholami Davoodi, Hosein Mohimani · 2020 · Lecture notes in computer science
73. Novel cyclic peptides from lethal Amanita species through a genomic approach, and major peptide toxins in the ectomycorrhizal association
    Hong Luo, Shengwen Zhou, Xincan Li, Xuan Li, Zuohong Chen, Zhu L. Yang, Li Guohong · 2020
74. Performing Selection on a Monotonic Function in Lieu of Sorting Using Layer-Ordered Heaps
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75. Minimalistic mycoplasmas harbor different functional toxin-antitoxin systems
    Virginia Hill, Hatice Akarsu, Rubén Sánchez Barbarroja, Valentina Cippà, Martin Heller, Laurent Falquet, Laurent Falquet, Michael Hubert Stoffel, Michael Hubert Stoffel, Joerg Jores · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
76. Sensitive and specific spectral library searching with COSS and Percolator
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77. Quantitative Label-Free Comparative Proteomic Analyses of Eukaryotic Tissues via Mass Spectrometry
    Kramer, David A · 2018 · ERA: Education and Research Archive (University of Alberta)
78. Computational Strategies for Proteogenomics Analyses
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79. A Machine-Learning-Based Algorithm for Peptide Feature Detection from Protein Mass Spectrometry Data
    Xiangyuan Zeng · 2021 · UWSpace (University of Waterloo)
80. Utilizing proteomics and phosphoproteomics to predict ex vivo drug sensitivity across genetically diverse AML patients
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81. Produção e caracterizção de enzimas celulolíticas a partir de resíduos agroindustriais pelo Aureobasidium pullulans LB 83 e sua respectiva análise proteômica
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82. Open search algorithms discover patterns of chemical modifications via LC-MS/MS
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83. Introduction to proteomics for chemical biology
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84. Evaluation of an integrative Bayesian peptide detection approach on a combinatorial peptide library
    Miroslav Hruska, Dušan Holub · 2021 · European Journal of Mass Spectrometry
85. Proteomics and Phosphoprotoemic Measurements Enhance Ability to Predict Ex Vivo Drug Response in AML
    Sara J.C. Gosline, Cristina E. Tognon, Michael D. Nestor, Sunil Kumar Joshi, Rucha V. Modak, Alisa Damnernsawad, Camilo Posso, Jamie Moon, Joshua Hansen, Chelsea M. Hutchinson-Bunch et al. · 2022 · Research Square
86. Proteomics
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87. The Musashi proteins are post-transcriptional activators of protein expression and alternative exon splicing in vertebrate photoreceptors
    Fatimah Kh. Matalkah, Bohye Jeong, Macie Sheridan, Eric James Horstick, Visvanathan Ramamurthy, Peter Stoilov · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
88. Evolutionary Algorithms for Improving De Novo Peptide Sequencing
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89. A Mass Spectrometry-Cleavable N-Terminal Tagging Strategy for System-Level Protease Activity Profiling
    Zixiang Fang, Maheshika S. K. Wanigasekara, Akop Yepremyan, Brandon Lam, Pawan Thapa, Frank W. Foss, Saiful M. Chowdhury · 2020 · ChemRxiv
90. Faculty Opinions recommendation of Native KCC2 interactome reveals PACSIN1 as a critical regulator of synaptic inhibition.
    Gerald Werner Zamponi · 2017 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
91. 蛋白质基因组学研究中的质谱仪与生物信息学方法
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92. Biological computing
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93. Metaproteomic Characterization of Forensic Samples
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94. A Deep Redox Proteome Profiling Workflow and Its Application to Skeletal Muscle of a Duchene Muscular Dystrophy Model
    Nicholas J. Day, Tong Zhang, Matthew J. Gaffrey, Rui Zhao, Thomas Fillmore, Ronald Jay Moore, George Gerald Rodney, Weijun Qian · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
95. Introduction to Mass Spectrometry Data
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96. High-Performance Computing Strategy Using Distributed-Memory Supercomputers
    Fahad Saeed, Muhammad Haseeb · 2022 · Computational biology
97. CDK4/6 inhibition and dsRNA sensor agonism co-operate to enhance anti-cancer effects through ER stress and immune modulation of tumour cells
    Victoria Roulstone, Joan Kyula, James Wright, Lu Yu, Aída Barreiro-Alonso, Miriam Melake, Jyoti Sharma Choudhary, Richard J. R. Elliott, Christopher J. Lord, David Mansfield et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
98. Integrating Identification and Quantification Uncertainty for Differential Protein Abundance Analysis with Triqler
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99. Multi-omics integration in Esophageal Adenocarcinoma reveals therapeutic targets and EAC-specific regulation of protein abundances
    J. Robert O’Neill, Marcos Yébenes Mayordomo, Goran Mitulović, Sofian Al Shboul, Georges Bedran, Jakub Faktor, Lenka Hernychová, Lukáš Uhrík, Maria Gómez-Herranz, Mikołaj Kocikowski et al. · 2022 · medRxiv