Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses

Rosenberger, George, Bludau, Isabell, Schmitt, Uwe, Heusel, Moritz, Hunter, Christie L, Liu, Yansheng, MacCoss, Michael J, MacLean, Brendan X +8 more·2017·Nature Methods
DOI 10.1038/nmeth.4398

Cited by (203)

Items 101–200 of 203

  1. Optimizing data‐independent acquisition (DIA) spectral library workflows for plasma proteomics studies
    Shawn J. Rice, Chandra Prakash Belani · 2022 · PROTEOMICS
  2. Proteotype coevolution and quantitative diversity across 11 mammalian species
    Qian Ba, Yuan‐Yuan Hei, Anasuya Dighe, Wenxue Li, Jamie D. Maziarz, Irene Pak, Shisheng Wang, Günter P. Wagner, Yansheng Liu · 2022 · Science Advances
  3. Apical anchorage and stabilization of subpellicular microtubules by apical polar ring ensures Plasmodium ookinete infection in mosquito
    Pengge Qian, Xu Wang, Cuirong Guan, Xin Fang, Mengya Cai, Chuan‐Qi Zhong, Yong Cui, Yanbin Li, Luming Yao, Huiting Cui et al. · 2022 · Nature Communications
  4. Proteogenomic Workflow Reveals Molecular Phenotypes Related to Breast Cancer Mammographic Appearance
    Tommaso De Marchi, Paul Theodor Pyl, Martin Sjöström, Stina Klasson, Hanna Sartor, Lena Tran, Gyula Pekár, Johan A. Malmström, Lars Malmström, Emma Niméus · 2021 · Journal of Proteome Research
  5. Circulating Exosome Involves in the Pathogenesis of Autoimmune Thyroid Diseases Through Immunomodulatory Proteins
    Xi Jia, Tianyu Zhai, Jin‐an Zhang · 2021 · Frontiers in Immunology
  6. Loss of β-cell identity and diabetic phenotype in mice caused by disruption of CNOT3-dependent mRNA deadenylation
    Dina Mostafa, Akiko Yanagiya, Eleni Georgiadou, Yibo Wu, Theodoros Stylianides, Guy A. Rutter, Toru Suzuki, Tadashi S. Yamamoto · 2020 · Communications Biology
  7. Proteomics analysis reveals suppression of IL-17 signaling pathways contributed to the therapeutic effects of Jia-Wei Bu-Shen-Yi-Qi formula in a murine asthma model
    Jingjing Qin, Tulake Wuniqiemu, Ying Wei, Fangzhou Teng, Jie Cui, Jing Sun, La Yi, Wei‐Feng Tang, Xueyi Zhu, Weifang Xu et al. · 2021 · Phytomedicine
  8. Generation of a murine SWATH-MS spectral library to quantify more than 11,000 proteins
    Chuan‐Qi Zhong, Jianfeng Wu, Xingfeng Qiu, Xi Chen, Changchuan Xie, Jiahuai Han · 2020 · Scientific Data
  9. Serum KLKB1 as a Potential Prognostic Biomarker for Hepatocellular Carcinoma Based on Data-Independent Acquisition and Parallel Reaction Monitoring
    Yi‐Qun Che, Yue Zhang, Han-Bing Li, Di Shen, Wei Cui · 2021 · Journal of Hepatocellular Carcinoma
  10. A peptide-centric approach to analyse quantitative proteomics data- an application to prostate cancer biomarker discovery
    Tânia Lima, João Eduardo Rodrigues, Bruno J. Manadas, Rui Henrique, Margarida Fardilha, Rui Miguel Pinheiro Vitorino · 2022 · Journal of Proteomics
  11. A Novel Blood Proteomic Signature for Prostate Cancer
    Ammara Muazzam, Matt P. Spick, Olivier Cexus, Bethany Geary, Fowz Azhar, Hardev Pandha, Agnieszka Michael, Rachel Reed, Sarah Lennon, Lee A. Gethings et al. · 2023 · Cancers
  12. Enhanced feature matching in single-cell proteomics characterizes IFN-γ response and co-existence of cell states
    Karl Kristian Krull, Syed Azmal Ali, Jeroen Krijgsveld · 2024 · Nature Communications
  13. Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis
    George Rosenberger, Wenxue Li, Mikko M. Turunen, Jing He, Prem S. Subramaniam, Sergey Pampou, Aaron Timothy Griffin, Charles Karan, Patrick Kerwin, Diana Murray et al. · 2024 · Nature Communications
  14. A data-independent acquisition (DIA)-based quantification workflow for proteome analysis of 5000 cells
    Na Jiang, Yan Ying Gao, Jia Xin Xu, Fengting Luo, Xiangyang Zhang, Ruibing Chen · 2022 · Journal of Pharmaceutical and Biomedical Analysis
  15. Systematic Assessment of the Effect of Internal Library in Targeted Analysis of SWATH-MS
    Chuan‐Qi Zhong, Rui Wu, Xi Chen, Suqin Wu, Jianwei Shuai, Jiahuai Han · 2019 · Journal of Proteome Research
  16. A proteomics analysis of the ovarian development in females of Haemaphysalis longicornis
    Minjing Wang, Yuhong Hu, Mengxue Li, Qianqian Xu, Xiaoli Zhang, Xiaoshuang Wang, Xiaomin Xue, Qi Xiao, Jingze Liu, Hui Wang · 2020 · Experimental and Applied Acarology
  17. Characterization of the Secretome, Transcriptome, and Proteome of Human β Cell Line EndoC-βH1
    Maria Ryaboshapkina, Kevin Saitoski, Ghaith M. Hamza, Andrew F. Jarnuczak, Sèverine Pechberty, Claire Berthault, Kaushik Sengupta, Christina Rye Underwood, Shalini Andersson, Raphaël Scharfmann · 2022 · Molecular & Cellular Proteomics
  18. Tear fluid proteomics: a comparative study of DIA and DDA mass spectrometry
    Saleh Ahmed, Jeremy Altman, Garrett Jones, Drew Mayernik, Eliza Williams, Amr S. Mahmoud, Tae Jin Lee, Wenbo Zhi, Shruti Sharma, Ashok Kumar Sharma · 2025 · Journal of Mass Spectrometry and Advances in the Clinical Lab
  19. The Generation of a Comprehensive Spectral Library for the Analysis of the Guinea Pig Proteome by SWATH‐MS
    Paweł Palmowski, Rachael Watson, G. Nicholas Europe‐Finner, Magdalena Karolczak‐Bayatti, Andrew Porter, Achim Treumann, Michael John Taggart · 2019 · PROTEOMICS
  20. MSLibrarian: Optimized Predicted Spectral Libraries for Data-Independent Acquisition Proteomics
    Marc Isaksson, Christofer A. Q. Karlsson, Thomas Laurell, Agnete Kirkeby, Moritz Heusel · 2022 · Journal of Proteome Research
  21. Using Two Peptide Isotopologues as Internal Standards for the Streamlined Quantification of Low-Abundance Proteins by Immuno-MRM and Immuno-MALDI
    Sahar Ibrahim, Bjoern C. Froehlich, Adriana Aguilar‐Mahecha, Raquel S. Aloyz, Oliver Poetz, Mark Basik, Gerald Batist, René Peiman Zahedi, Christoph H. Borchers · 2020 · Analytical Chemistry
  22. Anemonefishes: A model system for evolutionary genomics
    Marcela Herrera, Timothy Ravasi, Vincent Laudet · 2023 · F1000Research
  23. The Zea mays PeptideAtlas: A New Maize Community Resource
    Klaas Jan van Wijk, Tami Leppert, Zhi Sun, Isabell Guzchenko, Erica Debley, Georgia Sauermann, Pratyush Routray, Luis Mendoza, Qi Sun, Eric W. Deutsch · 2024 · Journal of Proteome Research
  24. QuantPipe: A User-Friendly Pipeline Software Tool for DIA Data Analysis Based on the OpenSWATH-PyProphet-TRIC Workflow
    Dazheng Wang, Guohong Gan, Xi Chen, Chuan‐Qi Zhong · 2020 · Journal of Proteome Research
  25. Diamond: a multi-modal DIA mass spectrometry data processing pipeline
    Chenxin Li, Mingxuan Gao, Wenxian Yang, Chuan‐Qi Zhong, Rongshan Yu · 2020 · Bioinformatics
  26. diaPASEF Enables High-Throughput Proteomic Analysis of Host Cell Proteins for Biopharmaceutical Process Development
    Taku Tsukidate, Alyssa Q. Stiving, Shannon Rivera, Ansuman Sahoo, Sri Ranganayaki Madabhushi, Xuanwen Li · 2024 · Analytical Chemistry
  27. Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework
    Matthias Fahrner, Melanie Christine Föll, Björn Andreas Grüning, Matthias Bernt, Hannes Luc Röst, Oliver Schilling · 2022 · GigaScience
  28. Toffee – a highly efficient, lossless file format for DIA-MS
    Brett Tully · 2020 · Scientific Reports
  29. Probing SWATH‐MS as a tool for proteome level quantification in a nonmodel fish
    Alison A. Monroe, Huoming Zhang, Celia Schunter, Timothy Ravasi · 2020 · Molecular Ecology Resources
  30. MSSort-DIAXMBD: A deep learning classification tool of the peptide precursors quantified by OpenSWATH
    Yiming Li, Qingzu He, Huan Guo, Chuan‐Qi Zhong, Li Xiang, Yulin Li, Jiahuai Han, Jianwei Shuai · 2022 · Journal of Proteomics
  31. Integration of data‐independent acquisition (DIA) with co‐fractionation mass spectrometry (CF‐MS) to enhance interactome mapping capabilities
    Brenna N. Hay, Mopelola O. Akinlaja, Teesha C. Baker, Aicha Asma Houfani, Richard Greg Stacey, Leonard J. Foster · 2023 · PROTEOMICS
  32. Data-Independent Acquisition Peptidomics
    Leon Bichmann, Shubham Gupta, Hannes Luc Röst · 2024 · Methods in molecular biology
  33. Achieving quantitative reproducibility in label-free multisite DIA experiments through multirun alignment
    Shubham Gupta, Justin Sing, Hannes Luc Röst · 2023 · Communications Biology
  34. Automated Workflow for Peptide-Level Quantitation from DIA/SWATH-MS Data
    Shubham Gupta, Hannes Luc Röst · 2021 · Methods in molecular biology
  35. Improved identification and quantification of peptides in mass spectrometry data via chemical and random additive noise elimination (CRANE)
    Akila J. Seneviratne, S. Peters, D. Clarke, Michael Dausmann, M. Hecker, B. Tully, P. Hains, Qing Zhong · 2021 · Bioinform.
  36. A Perspective on the Confident Comparison of Glycoprotein Site-Specific Glycosylation in Sample Cohorts
    Joshua Klein, Joseph Zaia · 2019 · Biochemistry
  37. iSwathX: an interactive web-based application for extension of DIA peptide reference libraries
    Zainab Noor, Jemma X. Wu, Dana Pascovici, Abidali Mohamedali, Mark P. Molloy, Mark S. Baker, Shoba Ranganathan · 2018 · Bioinformatics
  38. Generalized precursor prediction boosts identification rates and accuracy in mass spectrometry based proteomics
    Aaron M. Scott, Christofer A. Q. Karlsson, Tirthankar Mohanty, Erik Hartman, Suvi T. Vaara, Adam Linder, Johan A. Malmström, Lars Malmström · 2023 · Communications Biology
  39. One-stop analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform
    Fengchao Yu, Guo Ci Teo, Andy T. Kong, Klemens Fröhlich, Ginny Xiaohe Li, Vadim Demichev · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  40. Quantification of Dynamic Protein Interactions and Phosphorylation in LPS Signaling Pathway by SWATH-MS
    Xiurong Wu, Daowei Yang, Zhao Fu, Zhang‐Hua Yang, Dazheng Wang, Muzhen Qiao, Yuan Fang, Wanyun Li, Rui Wu, Peng He et al. · 2019 · Molecular & Cellular Proteomics
  41. The NtrYX Two-Component System of Paracoccus denitrificans Is Required for the Maintenance of Cellular Iron Homeostasis and for a Complete Denitrification under Iron-Limited Conditions
    Alfonso Olaya‐Abril, Víctor M. Luque‐Almagro, Jesús Hidalgo-Carrillo, Eduardo Chicano‐Gálvez, Francisco José Urbano, Conrado Moreno‐Vivián, David J. Richardson, María Dolores Roldán · 2022 · International Journal of Molecular Sciences
  42. Comprehensive Prostate Fluid-Based Spectral Libraries for Enhanced Protein Detection in Urine
    Annie Ha, Amanda Khoo, Vladimir Ignatchenko, Shahbaz Khan, Matthew Waas, Danny Vesprini, Stanley K. Liu, Julius O. Nyalwidhe, Oliver John Semmes, Paul Christopher Boutros et al. · 2024 · Journal of Proteome Research
  43. SWATH-MS as a strategy for CHO host cell protein identification and quantification supporting the characterization of mAb purification platforms
    Sofia B. Carvalho, Ludivine Profit, Sushmitha Krishnan, Ricardo A. Gomes, Bruno M. Alexandre, Séverine Clavier, Michael Hoffman, Kevin Brower, Patrícia Gomes‐Alves · 2024 · Journal of Biotechnology
  44. Multi-Reference Spectral Library Yields Almost Complete Coverage of Heterogeneous LC-MS/MS Data Sets
    Constantin Ammar, Evi Berchtold, Gergely Csaba, Andreas Schmidt, Axel Imhof, Ralf Zimmer · 2019 · Journal of Proteome Research
  45. Proteomics Mass Spectrometry Data Analysis Tools
    Aivett Bilbao Pena · 2018 · Elsevier eBooks
  46. Genomic, Proteomic and Phenotypic Heterogeneity in HeLa Cells across Laboratories: Implications for Reproducibility of Research Results
    Yansheng Liu, Mi Yang, Torsten Mueller, Saskia K. Kreibich, Evan G. Williams, Audrey van Drogen, Christelle Borel, Pierre‐Luc Germain, Max Frank, Isabell Bludau et al. · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  47. A Prostate Cancer Proteomics Database for SWATH-MS Based Protein Quantification
    Ammara Muazzam, Davide Chiasserini, Janet Kelsall, Nophar Geifman, Anthony David Whetton, Paul A. Townsend · 2021 · Cancers
  48. IonQuant enables accurate and sensitive label-free quantification with FDR-controlled match-between-runs
    Fengchao Yu, Sarah E. Haynes, Alexey I. Nesvizhskii · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  49. Definitive benchmarking of DDA and DIA for host cell protein analysis on the Orbitrap Astral in a regulatory-aligned framework
    Somar Khalil, Jenny T.C. Ho, Michel Plisnier · 2026 · Journal of Pharmaceutical and Biomedical Analysis Open
  50. Metatranscriptomics, Metaproteomics, and Metabolomics Approaches for Microbiome Characterization
    Anshu Mathuria, Kritika Jain, Ashok Saini, Chaitenya Verma, Indra Mani · 2024 · Springer eBooks
  51. Recent implementations of data-independent acquisition for cancer biomarker discovery in biological fluids
    Annie Ha, Michael Woolman, Matthew Waas, Meinusha Govindarajan, Thomas Kislinger · 2025 · Expert Review of Proteomics
  52. Proteomic-based biomarker discovery reveals panels of diagnostic biomarkers for early identification of heart failure subtypes
    Narainrit Karuna, Claire L. Tonry, Mark T. Ledwidge, Nadezhda Glezeva, Joe Gallagher, Kenneth McDonald, Chris J Watson · 2025 · Journal of Translational Medicine
  53. Advanced mass spectrometry-based methods for protein molecular-structural biologists
    Joanna Bons, Jacob Rose, Amy O’Broin, Birgit Schilling · 2022 · Elsevier eBooks
  54. Perspectives and opinions from scientific leaders on the evolution of data-independent acquisition for quantitative proteomics and novel biological applications
    Christie L. Hunter, Joanna Bons, Birgit Schilling · 2023 · Australian Journal of Chemistry
  55. DIAproteomics: A multi-functional data analysis pipeline for data-independent-acquisition proteomics and peptidomics
    Leon Bichmann, Shubham Gupta, George Rosenberger, Lèon Kuchenbecker, Timo T. Sachsenberg, Oliver Alka, Julianus Pfeuffer, Oliver Kohlbacher, Hannes Luc Röst · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  56. HLA Ligand Atlas DIA: extending the benign immunopeptidomics resource with increased sensitivity through data-independent acquisition mass spectrometry
    Leon Bichmann, Ana Marcu, Daniel Johannes Kowalewski, Lena Katharina Freudenmann, Linus Backert, Lena Mühlenbruch, Maren Lübke, Philipp Wagner, Tobias Engler, Sabine Matovina et al. · 2025 · Journal for ImmunoTherapy of Cancer
  57. MassDash: A Web-Based Dashboard for Data-Independent Acquisition Mass Spectrometry Visualization
    Justin Sing, Joshua Charkow, Mohammed AlHigaylan, Ira Horecka, Leon L. Xu, Hannes Luc Röst · 2024 · Journal of Proteome Research
  58. Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data
    Yichi Zhang, Chenghui Hu, Xiaohui Wu, Jian Song · 2024 · Bioinformatics
  59. Protocol for quantitative proteomic analysis of heterogeneous adipose tissue-residing progenitor subpopulations in mice
    Shan Bo, Clive S. Barker, Harry Theraulaz, Xiaoli Zhang, Yan Ping, Rana K. Gupta, Meng-Le Shao, Yibo Wu · 2023 · STAR Protocols
  60. Anemonefish Genomics
    Nicolas Salamin, Celia Schunter, Alison A. Monroe, Taewoo Ryu, Timothy Ravasi · 2022 · CRC Press eBooks
  61. A Case Study and Methodology for OpenSWATH Parameter Optimization Using the ProCan90 Data Set and 45 810 Computational Analysis Runs
    Sean M. Peters, Peter G. Hains, Natasha Lucas, Phillip James Robinson, Brett Tully · 2019 · Journal of Proteome Research
  62. A peptide-centric quantitative proteomics dataset for the phenotypic assessment of Alzheimer’s disease
    Gennifer E. Merrihew, Jea Park, Deanna L. Plubell, Brian C. Searle, Christopher Dirk Keene, Eric Berg Larson, Randall John Bateman, Richard J. Perrin, Jasmeer P. Chhatwal, Martin Rhys Farlow et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  63. A Statistical Approach for Identifying the Best Combination of Normalization and Imputation Methods for Label-Free Proteomics Expression Data
    Kabilan Sakthivel, S. B. Lal, Sudhir Srivastava, Krishna Kumar Chaturvedi, Yasin Jeshima Khan, Dwijesh Chandra Mishra, Sharanbasappa D Madival, Ramasubramanian Vaidhyanathan, Girish Kumar Jha · 2024 · Journal of Proteome Research
  64. Mass defect-based carbonyl activated tags (mdCATs) for multiplex data-independent acquisition proteome quantification
    Siwen Zhang, Yi Di, Jun Hu Yao, Yingjie Wang, Hong Shu, Guoquan Yan, Lei Zhang, Haojie Lu · 2020 · Chemical Communications
  65. A large‐scale assay library for targeted protein quantification in renal cell carcinoma tissues
    Petr Lapčík, Lucia Janáčová, Pavla Bouchalova, David Potěšil, Ján Podhorec, Milan Hora, Alexandr Poprach, Ondřej Fiala, Pavel Bouchal · 2021 · PROTEOMICS
  66. The Proteomics and Metabolomics of Pain
    David Gómez‐Varela, Manuela Schmidt · 2018 · Oxford University Press eBooks
  67. Estimating the Reliability of Low‐Abundant Signals and Limited Replicate Measurements through MS2 Peak Area in SWATH
    Franck Limonier, Sander Willems, Geneviève Waeterloos, Myriam Sneyers, Maarten Dhaenens, Dieter L. D. Deforce · 2018 · PROTEOMICS
  68. Mapping Cellular Microenvironments: Proximity Labeling and Complexome Profiling (Seventh Symposium of the Göttingen Proteomics Forum)
    Oliver Valerius, Abdul Rahman Asif, Tim Beißbarth, Rainer Bohrer, Hassan Dihazi, Kirstin Feussner, Olaf Jahn, Andrzej Majcherczyk, Bernhard Schmidt, Kerstin Schmitt et al. · 2019 · Cells
  69. Peak Detection On Data Independent Acquisition Mass Spectrometry Data With Semisupervised Convolutional Transformers
    Leon L. Xu, Hannes Luc Röst · 2020 · arXiv (Cornell University)
  70. Rapid profiling of protein complex re-organization in perturbed systems
    Isabell Bludau, Charlotte Nicod, Claudia Martelli, Peng Xue, Moritz Heusel, Andrea Fossati, Federico Uliana, Fabian Frommelt, Ruedi H. Aebersold, Ben C. Collins · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  71. Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis
    George Rosenberger, Wenxue Li, Mikko M. Turunen, Jing He, Prem S. Subramaniam, Sergey Pampou, Aaron Timothy Griffin, Charles Karan, Patrick Kerwin, Diana Murray et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  72. Integration of proteomics profiling data to facilitate discovery of cancer neoantigens: a survey
    Shifu Luo, Hui Peng, Ying Shi, Jiaxin Cai, Songming Zhang, Ning‐Yi Shao, Jinyan Li · 2025 · Briefings in Bioinformatics
  73. Harmonized Peptide Libraries Enable Practical Biofluid Selection for Developing Biomarker Assays
    Katelyn B Brusach, Ariana E. Shannon, Alex W. Joyce, Jessica M. Quimby, Brian C. Searle · 2025 · Molecular & Cellular Proteomics
  74. Scoring information integration with statistical quality control enhanced cross-run analysis of data-independent acquisition proteomics data
    Mingxuan Gao, Shubham Gupta, Wenxian Yang, Rongshan Yu, Hannes Luc Röst · 2025 · Communications Chemistry
  75. Developmental proteome dynamics in granulosa and thecal layers from growing follicles to pre-ovulatory duck follicles
    Weiguang Xia, Chenglong Jin, Shuang Wang, Yanan Zhang, Kaichao Li, Xuebing Huang, Chuntian Zheng, Wei Chen · 2025 · Biology of Reproduction
  76. Global impact of phosphorylation on protein endurance
    Chong-De Wu, Qian Ba, Wen-Xue Li, Barbora Šalovská, P. Hou, Torsten Mueller, George A. Rosenberger, Erli Gao, Yi Di, Yan-Sheng Liu · 2020 · bioRxiv
  77. Optimization of Spectral Library Size Improves DIA-MS Proteome Coverage
    Weigang Ge, Xiao Liang, Fangfei Zhang, Luang Xu, Nan Xiang, Rui Sun, Wei Liu, Zhangzhi Xue, Xiao Yi, Bo Wang et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  78. The role of metabolic profiling and dietary intervention in the early diagnosis and prevention of atherosclerosis
    Ali Khattib, Manar Shmet, Rasha Ashkar, Tony Hayek, Soliman Khatib · 2026 · Current Opinion in Lipidology
  79. Data-independent acquisition-based quantitative proteomics in plants
    X M Chen, Yuehua Chen, Wei Zhang, Mo‐Xian Chen, Patrick Willems, Fu‐Yuan Zhu · 2026 · Frontiers in Plant Science
  80. Integrative Multi-Omics Analysis of Multiple Sclerosis Reveals Cell-Type-Specific Regulatory Landscapes and Discordant Methylation–Expression Coupling
    Alper Bülbül, Özdeyiş Hülya Yılmaz-İşgördü, Manon Réda, Eda Tahir Turanlı · 2026 · International Journal of Molecular Sciences
  81. Generalized peakgroup scoring boosts identification rates and accuracy in mass spectrometry based discovery proteomics
    Aaron M. Scott, Christofer A. Q. Karlsson, Tirthankar Mohanty, Suvi T. Vaara, Adam Linder, Johan A. Malmström, Lars Malmström · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  82. ChatDIA: A zero-shot large language model workflow for targeted analysis of data-independent acquisition mass spectrometry data
    Jiayi Li, Joshua Charkow, Mingxuan Gao, Jiaqing Li, Hannes Luc Röst · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  83. Rapid Proteomic Screen of CRISPR Experiment Outcome by Data Independent Acquisition Mass Spectrometry: A Case Study for HMGN1
    Martin Mehnert, Wenxue Li, Chongde Wu, Barbora Šalovská, Yansheng Liu · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  84. A Proteogenomic Workflow Reveals Distinct Molecular Phenotypes Related to Breast Cancer Appearance
    Tommaso De Marchi, Paul Theodor Pyl, Martin Sjöström, Stina Klasson, Hanna Sartor, Johan A. Malmström, Lars Malmström, Emma Niméus · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  85. Proteotype Co-evolution and Diversity in Mammals
    Qian Ba, Yuan‐Yuan Hei, Anasuya Dighe, Wenxue Li, Jamie D. Maziarz, Irene Pak, Shisheng Wang, Günter P. Wagner, Yansheng Liu · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  86. Profiling Serum Intact N-Glycopeptides Using Data-Independent Acquisition Mass Spectrometry
    Yi Yang, Liang Qiao · 2023 · Methods in molecular biology
  87. Enhanced feature matching in single-cell proteomics characterizes response to IFN-γ and reveals co-existence of different cell states
    Karl Kristian Krull, Syed Azmal Ali, Jeroen Krijgsveld · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  88. An Equine Protein Atlas Highlights Synovial Fluid Proteome Dynamics during Experimentally LPS-Induced Arthritis
    Louise Bundgaard, Filip Årman, Emma Åhrman, Marie Walters, Ulrich auf dem Keller, Johan A. Malmström, Stine Bøttcher Jacobsen · 2024 · Journal of Proteome Research
  89. Cross-Run Hybrid Features Improve the Identification of Data-Independent Acquisition Proteomics
    Yachen Liu, Longfei Mei, Chenyu Liang, Chuan‐Qi Zhong, Mengsha Tong, Rongshan Yu · 2024 · ACS Omega
  90. Afamin and Apolipoprotein F Associated With Liver Steatosis From People Living With HIV : A Discovery Study
    Mario Frías, Eduardo Chicano‐Gálvez, Antonio Rivero‐Juárez, Ana Gordon, Diana Corona‐Mata, Jose M. Moyano, Ángela Peralbo‐Molina, Ángela Camacho, Ignacio Valero, Marı́a M. Malagón et al. · 2025 · Alimentary Pharmacology & Therapeutics
  91. Evaluation of the False Discovery Rate in Library-Free Search by DIA-NN Using In Vitro Human Proteome
    Kongxin Gu, Masanaga Kenko, Koji Ogawa, Naoki Goshima, Takeshi Masuda, Shingo Ito, Sumio Ohtsuki · 2025 · Journal of Proteome Research
  92. Complex assembly and activity states as multifaceted protein attributes explaining phenotypic variability
    George Rosenberger, Peng Xue, Isabell Bludau, Claudia Martelli, Evan G. Williams, Ben C. Collins, Andrea Califano, Yansheng Liu, Ruedi H. Aebersold · 2026 · Molecular Systems Biology
  93. Protein/peptide–drug conjugates: design, synthesis, and scale-up strategies of complex injectables
    Vijay Kumar, Diksha Khatkar, Pooja Jain, Aamir Mirza, Zeenat Iqbal · 2026 · Elsevier eBooks
  94. Pioneer and Altimeter: Fast Analysis of DIA Proteomics Data Optimized for Narrow Isolation Windows
    Nathan T. Wamsley, Emily Wilkerson, Michael B. Major, Dennis Goldfarb · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  95. Development of mass spectrometry-based analytical methods for a better quantification and a fine characterisation of proteomes
    Joanna Bons · 2019 · theses.fr (ABES)
  96. Développement de stratégies analytiques et bioinformatiques en protéomique quantitative : le défi de la quantification de protéines présentes à l’état de traces dans des mélanges biologiques d’extrêmes dynamique et complexité
    Nicolas Pythoud · 2020 · theses.fr (ABES)
  97. Full-DIA enables complete single-cell proteomics from diaPASEF using deep learning
    Jian Song, Amanda Momenzadeh, Hebin Liu, Chengpin Shen, Jesse G. Meyer, Xiaohui Wu · 2026 · Genome biology
  98. Reference-Based Library Construction Improves Performance in Low-input Workflows
    Joshua Charkow, Mahmoudreza Ghaznavi, Brendon Seale, Jiaxi Peng, Anne‐Claude Gingras, Hannes Luc Röst · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  99. Ground Truth–Based Evaluation of False Discovery Rate and Statistical Power in DIA Proteomics
    Jay M. Yarbro, Ya Huang, Vishwajeeth Pagala, Yingxue Fu, Zhen Wang, Long Wu, Xusheng Wang, Anthony A. High, Stephanie D. Byrum, Junmin Peng et al. · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  100. Tomato resistance to Phelipanche aegyptiaca by activation of reactive oxygen scavenging and phenylpropanoid metabolism
    Lu Zhang, Xiaolei Cao, Zhaoqun Yao, Qiuyue Zhao, Sifeng Zhao · 2026 · Industrial Crops and Products