MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

Ting, Lily, Rad, Ramin, Gygi, Steven P, Haas, Wilhelm·2011·Nature Methods
DOI 10.1038/nmeth.1714

Cited by (1,000)

Items 701–800 of 1,000

  1. Progress in Mass Spectrometry Acquisition Approach for Quantitative Proteomics
    Wei Zhang · 2014 · Chinese Journal of Analytical Chemistry
  2. Quantitative proteomics and terminomics to elucidate the role of ubiquitination and proteolysis in adaptive immunity
    Théo Klein, Rosa Viner, Christopher M. Overall · 2016 · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences
  3. Evaluating the Characteristics of Reporter Ion Signal Acquired in the Orbitrap Analyzer for Isobaric Mass Tag Proteome Quantification Experiments
    Christopher S. Hughes, Chenchen Zhu, Victor Spicer, Oleg V. Krokhin, Gregg B. Morin · 2017 · Journal of Proteome Research
  4. Identification of the S-transferase like superfamily bacillithiol transferases encoded by Bacillus subtilis
    Varahenage R. Perera, John D. Lapek, Gerald L. Newton, David J. Gonzalez, Kit Pogliano · 2018 · PLoS ONE
  5. Chronic platelet-derived growth factor receptor signaling exerts control over initiation of protein translation in glioma
    Shuang Ying Zhou, Vicky A. Appleman, Christopher M. Rose, Hyun Jung Jun, Juechen Yang, Yue Zhou, Roderick Terry Bronson, Steven P. Gygi, Alain Charest · 2018 · Life Science Alliance
  6. MS1-Level Proteome Quantification Platform Allowing Maximally Increased Multiplexity for SILAC and In Vitro Chemical Labeling
    Yeon Choi, Kyowon Jeong, Sanghee Shin, Joon Won Lee, Young-Suk Lee, Sangtae Kim, Sun Ah Kim, Jaehun Jung, Kwang Pyo Kim, V. Narry Kim et al. · 2020 · Analytical Chemistry
  7. Comparative Cell Surface Proteomic Analysis of the Primary Human T Cell and Monocyte Responses to Type I Interferon
    Lior Soday, Martin Potts, Leah M. Hunter, Benjamin J. Ravenhill, Jack W. Houghton, James C. Williamson, Robin Antrobus, Mark R. Wills, Nicholas J. Matheson, Michael P. Weekes · 2021 · Frontiers in Immunology
  8. Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia
    Jonathan D. Lee, João A. Paulo, Ryan R. Posey, Vera Mugoni, Nikki R. Kong, Giulia Cheloni, Yu-Ru Lee, Frank John Slack, Daniel Geoffrey Tenen, John G. Clohessy et al. · 2021 · Nature Methods
  9. NAD+ depletion enhances reovirus-induced oncolysis in multiple myeloma
    Barry E. Kennedy, Michael Giacomantonio, John Patrick Murphy, Samuel D. Cutler, Maryanne Sadek, Prathyusha Konda, João A. Paulo, Gopal P. Pathak, Saskia H.J. Renkens, Stacy Grieve et al. · 2022 · Molecular Therapy — Oncolytics
  10. Challenges Facing Complete Human Proteome Analysis
    Mio Iwasaki, Yasushi Ishihama · 2014 · Chromatography
  11. Quantitative Comparisons of Large Numbers of Human Plasma Samples Using TMT10plex Labeling
    Pengyuan Liu, Lynn A. Beer, Bonnie Ky, Kurt Thomas Barnhart, David W. Speicher · 2017 · Methods in molecular biology
  12. Brain Region-Specific nAChR and Associated Protein Abundance Alterations Following Chronic Nicotine and/or Menthol Exposure
    Matthew J. Mulcahy, Stephanie M. Huard, João A. Paulo, Jonathan H Wang, Sheri L. McKinney, Brandon J. Henderson, Henry A. Lester · 2019 · Journal of Proteome Research
  13. Library-free BoxCarDIA solves the missing value problem in label-free quantitative proteomics
    Devang Mehta, Sabine Scandola, R. Glen Uhrig · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  14. An RNA Damage Response Network Mediates the Lethality of 5-FU in Clinically Relevant Tumor Types
    Jung-Kuei Chen, Karl A. Merrick, Yi Wen Kong, Anita Izrael-Tomasevic, George M. Eng, Erika D. Handly, Jesse Christopher Patterson, Ian Gordon Cannell, Lucía Suárez-López, Aaron M. Hosios et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  15. Comprehensive Overview of Bottom-up Proteomics using Mass Spectrometry
    Yuming Jiang, Rex, Devasahayam Arokia Balaya, Dina Schuster, Benjamin A. Neely, Germán L. Rosano, Norbert Volkmar, Amanda Momenzadeh, Trenton M. Peters-Clarke, Susan Egbert, Simion D. Kreimer et al. · 2023 · PubMed
  16. Improved drug target deconvolution with PISA‐DIA using an extended, overlapping temperature gradient
    Samantha J. Emery‐Corbin, Jumana M. Yousef, Subash Adhikari, Fransisca Sumardy, Duong Nhu, Mark F. van Delft, Guillaume Lessène, Jerzy Michal Dziekan, Andrew Ian Webb, Laura F. Dagley · 2024 · PROTEOMICS
  17. 15N metabolic labeling-TMT multiplexing approach to facilitate the quantitation of glycopeptides derived from cell lines
    Mojgan Atashi, Peilin Jiang, Judith Ijeoma Nwaiwu, Cristian D. Gutierrez Reyes, Hanh Minh Thu Nguyen, Yunxiang Li, Parisa Ahmadi, Waziha Tasnim Purba, Yehia S. Mechref · 2024 · Analytical and Bioanalytical Chemistry
  18. Matrisome proteomics reveals novel mediators of muscle remodeling with aerobic exercise training
    Pattarawan Pattamaprapanont, Eileen M. Cooney, Tara L. MacDonald, João A. Paulo, Hui Pan, Jonathan M. Dreyfuss, Sarah J. Lessard · 2024 · Matrix Biology Plus
  19. Mapping the Cerebrospinal Fluid Proteome in Bipolar Disorder
    Andreas Göteson, Jessica Holmén‐Larsson, Hatice Celik, Aurimantas Pelanis, Carl M. Sellgren, Timea Sparding, Erik Pålsson, Henrik Zetterberg, Kaj Blennow, Lina Jönsson et al. · 2025 · Biological Psychiatry
  20. Spatial Proteome Reorganization of a Photosynthetic Model Cyanobacterium in Response to Abiotic Stresses
    Yan Wang, Haitao Ge, Zhen Xiao, Chengcheng Huang, Gaojie Wang, Xiaoxiao Duan, Li‐Min Zheng, Jinghui Dong, Xiahe Huang, Yuanya Zhang et al. · 2023 · Journal of Proteome Research
  21. Reverse-ChIP Techniques for Identifying Locus-Specific Proteomes: A Key Tool in Unlocking the Cancer Regulome
    Tim M.G. MacKenzie, Rocío Cisneros, Rajan Douglas Maynard, Michael P. Snyder · 2023 · Cells
  22. TMEM106B reduction does not rescue GRN deficiency in iPSC-derived human microglia and mouse models
    Sara L. Domínguez, Benjamin I. Laufer, Arundhati Sengupta Ghosh, Qingling Li, Gaia Ruggeri, Maheswarareddy Emani, Lilian Phu, Brad A. Friedman, Wendy N. Sandoval, Christopher M. Rose et al. · 2023 · iScience
  23. 102-Plex Approach for Accurate and Multiplexed Proteome Quantification
    Zhen Wu, Xirui Huang, Lin Huang, Xumin Zhang · 2024 · Analytical Chemistry
  24. Carboxyl-Ester Lipase Maturity-Onset Diabetes of the Young Disease Protein Biomarkers in Secretin-Stimulated Duodenal Juice
    Yngvild Bjørlykke, Heidrun Vethe, Marc Vaudel, Harald Barsnes, Frode S. Berven, Erling Tjora, Helge Ræder · 2014 · Journal of Proteome Research
  25. Quantitative proteomics in Giardia duodenalis —Achievements and challenges
    Samantha J. Emery‐Corbin, Ernest Lacey, Paul A. Haynes · 2016 · Molecular and Biochemical Parasitology
  26. Proteomics of Eosinophil Activation
    D. Mosher, Emily M. Wilkerson, Keren B. Turton, Alexander S. Hebert, J. Coon · 2017 · Frontiers in Medicine
  27. Association of tricellulin expression with poor colorectal cancer prognosis and metastasis
    Jin‐Xiu Zhang, Mengbin Qin, Zhe Ye, Peng Peng, Siman Li, Qian Song, Lan Lin, Shiquan Liu, Lihua Xie, Ye Zhu et al. · 2020 · Oncology Reports
  28. Integrative description of changes occurring on zebrafish embryos exposed to water-soluble crude oil components and its mixture with a chemical surfactant
    Carlos Eduardo González-Penagos, Jesús Alejandro Zamora‐Briseño, Mónica Améndola-Pimenta, José M. Elizalde‐Contreras, Flor Árcega-Cabrera, Yanis Cruz‐Quintana, Ana María Santana‐Piñeros, Mayra Alejandra Cañizares-Martínez, Juan Antonio Pérez-Vega, Eliel Ruíz-May et al. · 2022 · Toxicology and Applied Pharmacology
  29. Isobaric Stable Isotope N‐Phosphorylation Labeling (iSIPL) for Ultrasensitive Proteome Quantification
    Xiaoyu Wang, Chun‐Jing Chen, Yaohui He, Lian‐Shuai Ding, Yifan Wu, Cheng‐Ting Huang, Jun Wu, Rong Ding, Yuhua Xue, Zhi‐Wei Lin et al. · 2023 · Angewandte Chemie International Edition
  30. MilQuant: A free, generic software tool for isobaric tagging-based quantitation
    Xiao Zou, Minzhi Zhao, Hongyan Shen, Xuyang Zhao, Yuanpeng Tong, Qingsong Wang, Shicheng Wei, Jianguo Ji · 2012 · Journal of Proteomics
  31. Quantitative Proteomic Approaches in Mouse: Stable Isotope Incorporation by Metabolic (SILAC) or Chemical Labeling (Reductive Dimethylation) Combined with High‐Resolution Mass Spectrometry
    Anja M. Billing, Hisham Ben Hamidane, Johannes Graumann · 2015 · Current Protocols in Mouse Biology
  32. Neuroproteomics — LC-MS Quantitative Approaches
    Cátia Santa, Sandra Isabel Anjo, Vera M. Mendes, Bruno J. Manadas · 2015 · InTech eBooks
  33. Targeted histidine-peptide enrichment improved the accuracy of isobaric-based quantitative proteomics
    Jingjing Yang, Tian Fang, Manli Zhang, Yang Chun Zhao, Xiaohong Qian, Yun Cai, Wantao Ying · 2016 · Analytical Methods
  34. In vitro assembly and proteomic analysis of RNA polymerase II complexes
    Yoo Jin Joo, Scott B. Ficarro, Jarrod A. Marto, Stephen Buratowski · 2019 · Methods
  35. Proteomic Approaches for Advancing the Understanding and Application of Oleaginous Bacteria for Bioconversion of Lignin to Lipids
    Xiaolu Li, Zhangyang Xu, Austin Gluth, Weijun Qian, Bin Yang · 2021 · ACS symposium series
  36. New advances in quantitative proteomics research and current applications in asthma
    Yanting Lan, Xiaoyin Zeng, Jing Xiao, Longbo Hu, Long Tan, Mengdi Liang, Xufei Wang, Shaohua Lu, Fei Long, Tao Peng · 2021 · Expert Review of Proteomics
  37. Up-regulation of the PI3K/AKT and RHO/RAC/PAK signalling pathways in CHK1 inhibitor resistant Eµ-Myc lymphoma cells
    Jill E. Hunter, Amy E. Campbell, Scott T. Kerridge, Callum J. Fraser, Nicola L. Hannaway, Saimir Luli, Iglika G. Ivanova, Philip Brownridge, Jonathan M Coxhead, Leigh Taylor et al. · 2022 · Biochemical Journal
  38. Comparison of data analysis parameters and MS/MS fragmentation techniques for quantitative proteome analysis using isobaric peptide termini labeling (IPTL)
    Christian Jeffrey Koehler, Magnus Ø. Arntzen, Achim Treumann, Bernd Thiede · 2012 · Analytical and Bioanalytical Chemistry
  39. Organ-level protein networks as a reference for the host effects of the microbiome
    Robert H. Mills, Jacob M. Wozniak, Alison F. Vrbanac, Anaamika Campeau, Benoît Chassaing, Andrew T. Gewirtz, Rob D. Knight, David J. Gonzalez · 2020 · Genome Research
  40. Global Protein-Turnover Quantification in Escherichia coli Reveals Cytoplasmic Recycling under Nitrogen Limitation
    Meera Gupta, Alex N. T. Johnson, Edward R. Cruz, Eli J. Costa, Randi L. Guest, Hsin‐Jung Li, Elizabeth M. Hart, Thao Nguyen, Michael Stadlmeier, Benjamin P. Bratton et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  41. Proteome-Wide Profiling Using Sample Multiplexing of a Human Cell Line Treated with Cannabidiol (CBD) and Tetrahydrocannabinol (THC)
    Morteza Abyadeh, Vivek Gupta, Xinyue Liu, Valentina Rossio, Mehdi Mirzaei, Jennifer Louise Cornish, João A. Paulo, Paul A. Haynes · 2023 · Proteomes
  42. Profiling Proteins and Phosphorylation Sites During T Cell Activation Using an Integrated Thermal Shift Assay
    Brandon M. Gassaway, Edward L. Huttlin, Emily M. Huntsman, Tomer M. Yaron-Barir, Jared Lee Johnson, Kiran Kurmi, Lewis C. Cantley, João A. Paulo, Alison Epstein Ringel, Steven P. Gygi et al. · 2024 · Molecular & Cellular Proteomics
  43. Methodologies for Measuring Protein Trafficking across Cellular Membranes
    Ziqi Lyu, Joseph C. Genereux · 2021 · ChemPlusChem
  44. Infrared Photoactivation Boosts Reporter Ion Yield in Isobaric Tagging
    Kenneth W. Lee, Trenton M. Peters-Clarke, Keaton L. Mertz, Graeme C. McAlister, John E. P. Syka, Michael S. Westphall, Joshua J. Coon · 2022 · Analytical Chemistry
  45. Comparative Assessment of Quantification Methods for Tumor Tissue Phosphoproteomics
    Yang Zhang, Benjamin Dreyer, Natalia I. Govorukhina, Alexander Martin Heberle, Saša Končarević, Christoph Krisp, Christiane A. Opitz, Pauline Pfänder, Rainer Bischoff, Hartmut Schlüter et al. · 2022 · Analytical Chemistry
  46. Proteomic changes associated with racial background and sepsis survival outcomes
    Kathryn L. Kapp, Albert B. Arul, Kevin C Zhang, Liping Du, Sachin P. Yende, John A. Kellum, Derek C. Angus, Octavia M. Peck‐Palmer, Renã A. S. Robinson · 2022 · Molecular Omics
  47. Characterization of huntingtin interactomes and their dynamic responses in living cells by proximity proteomics
    Hongyuan Xu, Johanna Bensalel, Sunil Raju, Enrico Capobianco, Michael L. Lu, Jianning Wei · 2022 · Journal of Neurochemistry
  48. Proteomic analysis of antiviral innate immunity
    Jonas Dutra Albarnaz, Michael P. Weekes · 2022 · Current Opinion in Virology
  49. Measurement and utilization of the proteomic reactivity by mass spectrometry
    Clodette Punzalan, Lei Wang, Bekim Bajrami, Xudong Yao · 2023 · Mass Spectrometry Reviews
  50. Improved Structural Characterization of Glycerophospholipids and Sphingomyelins with Real-Time Library Searching
    Dain R. Brademan, Katherine A. Overmyer, Yuchen He, William D. Barshop, Jesse D. Canterbury, Brandon J. Bills, Benton J. Anderson, Paul D. Hutchins, S. Sharma, Vlad Zabrouskov et al. · 2023 · Analytical Chemistry
  51. Primate cerebrospinal fluid CHI3L1 reflects brain TREM2 agonism
    Stephen P. Schauer, Chang Hoon Cho, Gloriia Novikova, Gillie A. Roth, Julie Lee, Anup Dutt Sharma, Alejandro R. Foley, Carl Ng, Philip Shen, Meena Choi et al. · 2024 · Alzheimer s & Dementia
  52. Proteomic Profiling of Ovarian Cancer Models Using TMT-LC-MS/MS
    John Sinclair, John F. Timms · 2013 · Methods in molecular biology
  53. Assessing the Phagosome Proteome by Quantitative Mass Spectrometry
    Julien Peltier, Anetta Härtlová, Matthias Trost · 2016 · Methods in molecular biology
  54. Quantitative Performance Evaluator for Proteomics (QPEP): Web-based Application for Reproducible Evaluation of Proteomics Preprocessing Methods
    Dario Strbenac, Ling Zhong, Mark J. Raftery, Penghao Wang, Susan R. Wilson, Nicola J. Armstrong, Jean Yee Hwa Yang · 2017 · Journal of Proteome Research
  55. Proteomics in the Study of Liver Diseases
    Lili Niu, Philipp Emanuel Geyer, Matthias Mann · 2018 · Springer eBooks
  56. Quantitative Proteome Responses to Oncolytic Reovirus in GM-CSF- and M-CSF-Differentiated Bone Marrow-Derived Cells
    Michael Giacomantonio, Andra Mihaela Sterea, Youra Kim, João A. Paulo, Derek R. Clements, Barry E. Kennedy, Moamen Bydoun, Ge Shi, David M. Waisman, Steven P. Gygi et al. · 2019 · Journal of Proteome Research
  57. Impact of Zika virus on the human type I interferon osteoimmune response
    Arnaud C. Drouin, Nicholas J. Wallbillich, Marc Theberge, Sharon Liu, Joshua Katz, Kamela Bellovoda, Scarlett Se Yun Cheon, Frederick Gootkind, Emily Bierman, Jason Zavras et al. · 2020 · Cytokine
  58. Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage
    Ching-Tai Chen, Jen-Hung Wang, Cheng-Wei Cheng, Wei-Che Hsu, Chu-Ling Ko, Wai-Kok Choong, Ting‐Yi Sung · 2021 · Scientific Reports
  59. A1 Ions: Peptide-Specific and Intensity-Enhanced Fragment Ions for Accurate and Multiplexed Proteome Quantitation
    Jianhui Liu, Yuan Zhou, Xinhang Hou, Chao Liu, Baofeng Zhao, Yichu Shan, Zhigang Sui, Zhen Liang, Lihua Zhang, Yukui Zhang · 2022 · Analytical Chemistry
  60. Endogenous protein interactomes resolved through immunoprecipitation-coupled quantitative proteomics in cell lines
    Raman Kumar, Karthik Shantharam Kamath, Luke Carroll, Peter Hoffmann, Jozef Gécz, Lachlan A. Jolly · 2022 · STAR Protocols
  61. Apolipoprotein E is a pancreatic extracellular factor that maintains mature β-cell gene expression
    Ahmed I. Mahmoud, Francisco X. Galdos, Katherine A. Dinan, Mark P. Jedrychowski, Jeffrey C. Davis, Ana Vujić, Inbal Rachmin, Christian Shigley, James R. Pancoast, Samuel Lee et al. · 2018 · PLoS ONE
  62. Quantitative Proteomics for Differential Protein Expression Profiling
    Christian Karl Frese, Henk van den Toorn, Albert J. R. Heck, Shabaz Mohammed · 2019 · Wiley eBooks
  63. The Breast Cancer Proteome and Precision Oncology
    Jonathan Thomas Lei, Eric J. Jaehnig, Hannah L. Smith, Matthew Valle Holt, Xi Li, Meenakshi Anurag, Matthew J. Ellis, Gordon Brent Mills, Bing Zhang, Marilyne Labrie · 2023 · Cold Spring Harbor Perspectives in Medicine
  64. Tight regulation of a nuclear HAPSTR1-HUWE1 pathway essential for mammalian life
    David R. Amici, Sammy Alhayek, Austin T Klein, Yizhi Wang, Anika P. Wilen, Weimin Song, Pei Zhu, Abhishek Vijay Thakkar, McKenzi A King, Adam W. T. Steffeck et al. · 2024 · Life Science Alliance
  65. The E3 ligase HECTD4 regulates COX-2-dependent tumor progression and metastasis
    Joanna A. Vuille, Cem Tanrıöver, Ezgi Antmen, Douglas Scott Micalizzi, Richard Y. Ebright, Sambhavi Animesh, Robert Tyler Morris, Soroush Hajizadeh, Zachary J. Nicholson, Hunter C. Russell et al. · 2025 · Proceedings of the National Academy of Sciences
  66. Sensitive and Accurate Proteome Profiling of Embryogenesis Using Real-Time Search and TMTproC Quantification
    Alex N. T. Johnson, Jingjing Huang, Argit Marishta, Edward R. Cruz, Andrea Mariossi, William D. Barshop, Jesse D. Canterbury, Rafael Donadelli Melani, David Bergen, Vlad Zabrouskov et al. · 2024 · Molecular & Cellular Proteomics
  67. Uncovering dynamic phosphorylation signaling using mass spectrometry
    Hannah Johnson · 2015 · International Journal of Mass Spectrometry
  68. Protected Amine Labels: A Versatile Molecular Scaffold for Multiplexed Nominal Mass and Sub-Da Isotopologue Quantitative Proteomic Reagents
    Scott B. Ficarro, Jessica M. Biagi, Jinhua Wang, Jenna Scotcher, Rositsa Koleva, Joseph D. Card, Guillaume Adelmant, Huan He, Manor Askenazi, Alan G. Marshall et al. · 2014 · Journal of the American Society for Mass Spectrometry
  69. Spatial Proteomics: Practical Considerations for Data Acquisition and Analysis in Protein Subcellular Localisation Studies
    Andy Christoforou, Claire M. Mulvey, Lisa M. Breckels, Laurent Gatto, Kathryn Susan Lilley · 2014 · Royal Society of Chemistry eBooks
  70. Accurate quantification of modified cyclic peptides without the need for authentic standards
    Rosemary I. Adaba, Greg Mann, Andrea Raab, Wael E. Houssen, Andrew R. McEwan, Louise Thomas, Jioji N. Tabudravu, James H. Naismith, Marcel Jaspars · 2016 · Tetrahedron
  71. PTU, a novel ureido-fatty acid, inhibits MDA-MB-231 cell invasion and dissemination by modulating Wnt5a secretion and cytoskeletal signaling
    Yassir Al-Zubaidi, Yongjuan Chen, Md. Khalilur Rahman, Bala Umashankar, Hassan Choucair, Kirsi Bourget, Long Hoa Chung, Yanfei Qi, Paul Kenneth Witting, Robin L. Anderson et al. · 2021 · Biochemical Pharmacology
  72. Glycoprotein Pathways Altered in Frontotemporal Dementia With Autoimmune Disease
    Fiona Bright, Jared S. Katzeff, John R. Hodges, Olivier Piguet, Jillian J. Kril, Glenda Margaret Halliday, Woojin Scott Kim · 2021 · Frontiers in Immunology
  73. Skeletal muscle proteome expression differentiates severity of cancer cachexia in mice and identifies loss of fragile X mental retardation syndrome‐related protein 1
    Andy V. Khamoui, Dorota Tokmina‐Roszyk, Rafaela G. Feresin, Gregg B. Fields, Nishant P. Visavadiya · 2022 · Proteomics
  74. Petroleum coke exposure leads to altered secretome profiles in human lung models
    Joseph A. Caruso, Paul M. Stemmer · 2018 · Human & Experimental Toxicology
  75. Adiporedoxin, an upstream regulator of ER oxidative folding and protein secretion in adipocytes
    Mark P. Jedrychowski, Libin Liu, Collette J Laflamme, Kalypso Karastergiou, Tova Meshulam, Shi-Ying Ding, Yuanyuan Wu, Mi‐Jeong Lee, Steven P. Gygi, Susan K. Fried et al. · 2015 · Molecular Metabolism
  76. MAGMa: Your Comprehensive Tool for Differential Expression Analysis in Mass-Spectrometry Proteomic Data
    Shagun Gupta, Jin Joo Kang, Yu Sun, Kumar Yugandhar, Mateusz Maciej Wagner, William J. Comstock, James G. Booth, Marcus Bustamante Smolka, Haiyuan Yu · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  77. MSFragger-DDA+ Enhances Peptide Identification Sensitivity with Full Isolation Window Search
    Fengchao Yu, Yamei Deng, Alexey I. Nesvizhskii · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
  78. COP1 Deficiency in BRAFV600E Melanomas Confers Resistance to Inhibitors of the MAPK Pathway
    Ada Ndoja, Christopher M. Rose, Eva Lin, Rohit Reja, Jelena Petrovic, Sarah Kummerfeld, Andrew P. Blair, Helen Rizos, Zora D. Modrusan, Scott E. Martin et al. · 2025 · Cells
  79. Protein isolates derived from pea seeds pre-treated with radio frequency: Changes in global proteomes and impacts on nutritional and functional properties
    Prem Prakash Das, Yuping Lu, Li Liu, Praiya Asavajaru, Darrin Klassen, Caishuang Xu, Allaoua Achouri, Mélanie Pitre, Caroline Lapointe, Lamia L’Hocine et al. · 2025 · LWT
  80. A comprehensive review on tandem mass tag based proteomics deciphering molecular insights of fruit development and ripening
    Sibani Sahoo, Arpita Jena, Dinesh Pradhan, Giridara‐Kumar Surabhi · 2026 · Discover Plants.
  81. Ca2+-Triggered (de)ubiquitination Events in Synapses
    Sofia Ainatzi, Svenja V. Kaufmann, Ivan Silbern, Svilen Veselinov Georgiev, Sonja Lorenz, Silvio O. Rizzoli, Henning Urlaub · 2025 · Molecular & Cellular Proteomics
  82. Differences in the Abundance of Auxin Homeostasis Proteins Suggest Their Central Roles for In Vitro Tissue Differentiation in Coffea arabica
    Ana Odetth Quintana-Escobar, Hugo A. Méndez-Hernández, Rosa María Galaz-Ávalos, José M. Elizalde‐Contreras, Francisco Antonio Reyes-Soria, Victor Aguilar‐Hernández, Eliel Ruíz-May, Victor Manuel Loyola-Vargas · 2021 · Plants
  83. Determining DNA–Protein Binding Affinities and Specificities from Crude Lysates Using a Combined SILAC/TMT Labeling Strategy
    Cathrin Gräwe, Miguel Hernández-Quiles, Pascal W.T.C. Jansen, Annika Brimmers, Michiel Vermeulen · 2023 · Journal of Proteome Research
  84. IQMMA: Efficient MS1 Intensity Extraction Pipeline 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 · Journal of Proteome Research
  85. Pleiotropic tumor suppressive functions of PTEN missense mutations during gliomagenesis
    Hyun Jung Jun, João A. Paulo, Victoria A. Appleman, Tomer M. Yaron, Jared Lee Johnson, Alan T. Yeo, Vaughn A. Rogers, Shan Kuang, Hemant Varma, Steven P. Gygi et al. · 2024 · iScience
  86. Characterizing protein-protein interactions with thermal proteome profiling
    Brian C. Searle · 2024 · Current Opinion in Structural Biology
  87. A Multipoint Validation of Quantification in Capillary Electrophoresis Mass Spectrometry Proteomics: Isobaric Multiplexing with Tandem Mass Tags
    Laura G. Rodriguez, Camille Lombard‐Banek, Vi M. Quach, Sam B. Choi, M. Chiara Manzini, Péter Nemes · 2025 · Analytical Chemistry
  88. Phosphoproteomics in photosynthetic organisms
    William O. Slade, Emily Grace Werth, Alex Chao, Leslie M. Hicks · 2014 · Electrophoresis
  89. Proteomics quantification of protein nitration
    Adam R. Evans, Renã A. S. Robinson · 2013 · Reviews in Analytical Chemistry
  90. Sensing Small Changes in Protein Abundance: Stimulation of Caco-2 Cells by Human Whey Proteins
    Judy K. Cundiff, Elizabeth J. McConnell, Kimberly Lohe, Sarah Maria, Robert J. McMahon, Qıang Zhang · 2015 · Journal of Proteome Research
  91. A New Era of Protein-Based Assays for Cancer Early Detection
    Lecia Van Dam Sequist, Steven J. Skates, Wilhelm Haas · 2021 · Journal of Thoracic Oncology
  92. Quantifying Proteome and Protein Modifications in Activated T Cells by Multiplexed Isobaric Labeling Mass Spectrometry
    Haiyan Tan, Daniel Bastardo Blanco, Boer Xie, Yuxin Li, Zhiping Wu, Hongbo Chi, Junmin Peng · 2021 · Methods in molecular biology
  93. Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses
    Swetha Rajasekaran, Jalal Siddiqui, Jessica B. Rakijas, Brandon Nicolay, Chenyu Lin, Eshan Khan, Rahi Patel, Robert Tyler Morris, Emanuel Wyler, Myriam Boukhali et al. · 2021 · Communications Biology
  94. High-Throughput Proteome Profiling of Plasma and Native Plasma Complexes Using Native Chromatography
    Aleksandr Gaun, Niclas Olsson, John C. K. Wang, Dan Eaton, Fiona Elizabeth McAllister · 2023 · Methods in molecular biology
  95. Endothelial intercellular cell adhesion molecule 1 contributes to cell aggregate formation in CHO cells cultured in serum‐free media
    Salina Louie, Amy J. Heidersbach, Noelia Blanco, Benjamin Haley, Christopher M. Rose, Peter S. Liu, Mandy Yim, Danming Tang, Cynthia Lam, Wendy N. Sandoval et al. · 2019 · Biotechnology Progress
  96. Parallel proteomic and phosphoproteomic analyses reveal cellobiose‐dependent regulation of lignocellulase secretion in the filamentous fungus Neurospora crassa
    Bentao Xiong, Linfang Wei, Yifan Wang, Jinyu Li, Xin Liu, Yunheng Zhou, Panpan Du, Hao Fang, Johannes Liesche, Yahong Wei et al. · 2021 · GCB Bioenergy
  97. Global Proteome Profiling to Assess Changes in Protein Abundance Using Isobaric Labeling and Liquid Chromatography-Tandem Mass Spectrometry
    Anthony P. Possemato, Kathryn Abell, Matthew P. Stokes · 2021 · Methods in molecular biology
  98. MS 3 ‐based quantitative proteomics using pulsed‐Q dissociation
    Zhiyun Cao, Adam R. Evans, Renã A. S. Robinson · 2015 · Rapid Communications in Mass Spectrometry
  99. S-Nitrosylation in Alzheimer’s Disease Using Oxidized Cysteine-Selective cPILOT
    Ryan Robert Dyer, Liqing Gu, Renã A. S. Robinson · 2017 · Neuromethods
  100. Stable Protein Gel Storage in Acetonitrile for Mass Spectrometric Analysis
    Yuxin Chen, Sen Wang, Jia Jia, Xinyu Tian, Hongpan Xu, Mingzhe Ning, Bing Bai · 2018 · PROTEOMICS