Protein Analysis by Shotgun/Bottom-up Proteomics
Zhang, Yaoyang, Fonslow, Bryan R., Shan, Bing, Baek, Moon-Chang, Yates, John R.·2013·Chemical Reviews
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- Overview and Considerations in Bottom-Up ProteomicsRachel M. Miller, L. Smith · 2022 · In Analysis
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- Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometryP. Boomathi Pandeswari, Varatharajan Sabareesh · 2019 · RSC Advances
- One-Tip enables comprehensive proteome coverage in minimal cells and single zygotesZilu Ye, Pierre Sabatier, Javier Martin Gonzalez, Akihiro Eguchi, Maico Y. Lechner, Ole Østergaard, Jingsheng Xie, Yuan Guo, Lesley Schultz, Rafaela Truffer et al. · 2024 · Nature Communications
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- Mass Spectrometry in Plant-omicsErin Gemperline, Caitlin Keller, Lingjun Li · 2016 · Analytical Chemistry
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- Mapping the Energetic Epitope of an Antibody/Interleukin-23 Interaction with Hydrogen/Deuterium Exchange, Fast Photochemical Oxidation of Proteins Mass Spectrometry, and Alanine Shave MutagenesisJing Li, Hui Wei, Stanley R. Krystek, Derek Bond, Ty Brender, Daniel Cohen, Jena Feiner, Nels B. Hamacher, Johanna Harshman, Richard Y.‐C. Huang et al. · 2017 · Analytical Chemistry
- Extensive and Accurate Benchmarking of DIA Acquisition Methods and Software Tools Using a Complex Proteomic StandardClarisse Gotti, Florence Roux‐Dalvai, Charles Joly-Beauparlant, Loïc Mangnier, Mickaël Leclercq, Arnaud Droit · 2021 · Journal of Proteome Research
- An in-depth snake venom proteopeptidome characterization: Benchmarking Bothrops jararacaCarolina Alves Nicolau, Paulo C. Carvalho, Inácio L.M. Junqueira-de-Azevedo, André Teixeira‐Ferreira, Magno Junqueira, Jonás Perales, Ana Gisele C. Neves‐Ferreira, Richard Hemmi Valente · 2016 · Journal of Proteomics
- Instrumentation at the Leading Edge of ProteomicsTrenton M. Peters-Clarke, Joshua J. Coon, Nicholas McIlvain Riley · 2024 · Analytical Chemistry
- Considerations for constructing a protein sequence database for metaproteomicsJ. Alfredo Blakeley‐Ruiz, Manuel Kleiner · 2022 · Computational and Structural Biotechnology Journal
- Thousand and one ways to quantify and compare protein abundances in label-free bottom-up proteomicsMélisande Blein‐Nicolas, Michel Zivy · 2016 · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
- Proteopeptidomic, Functional and Immunoreactivity Characterization of Bothrops moojeni Snake Venom: Influence of Snake Gender on Venom CompositionFernanda Gobbi Amorim, Tássia R. Costa, Dominique Baiwir, Edwin De Pauw, Loïc Quinton, Suely Vilela Sampaio · 2018 · Toxins
- Applications of Copper-Catalyzed Click Chemistry in Activity-Based Protein ProfilingJulianne Martell, Eranthie Weerapana · 2014 · Molecules
- Applications and challenges of forensic proteomicsEric D. Merkley, David S. Wunschel, Karen L. Wahl, Kristin H. Jarman · 2019 · Forensic Science International
- Physicochemical characterization of biopharmaceuticalsMaria Kristina Parr, Othman Montacir, Houda Montacir · 2016 · Journal of Pharmaceutical and Biomedical Analysis
- Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methodsMichiel van de Waterbeemd, Sem Tamara, Kyle L. Fort, Eugen Damoc, Vojtěch Franc, P. Bieri, Martin Peter Itten, Alexander Makarov, Nenad Ban, Albert J. R. Heck · 2018 · Nature Communications
- Challenges and Advances in the Fabrication of Monolithic Bioseparation Materials and their Applications in Proteomics ResearchShujuan Ma, Ya Li, Chen Ma, Yan Wang, Junjie Ou, Mingliang Ye · 2019 · Advanced Materials
- Proper imputation of missing values in proteomics datasets for differential expression analysisMingyi Liu, Ashok R. Dongré · 2020 · Briefings in Bioinformatics
- Single-cell omics: experimental workflow, data analyses and applicationsFengying Sun, Haoyan Li, Dongqing Sun, Shaliu Fu, Lei Gu, Xin Shao, Qinqin Wang, Xin Dong, Bin Duan, Feiyang Xing et al. · 2024 · Science China Life Sciences
- GeLC-MS/MS Analysis of Complex Protein MixturesMonika Dzieciątkowska, Ryan C. Hill, Kirk Charles Hansen · 2014 · Methods in molecular biology
- MS-Based Proteomic Analysis of Serum and Plasma: Problem of High Abundant Components and Lights and Shadows of Albumin RemovalMonika Pietrowska, Agata Wlosowicz, Marta Gawin, Piotr Widłak · 2019 · Advances in experimental medicine and biology
- Exploiting Interactions between Polyoxometalates and Proteins for Applications in (Bio)chemistry and MedicineSarah Lentink, David E. Salazar Marcano, Mhamad Aly Moussawi, Tatjana N. Parac‐Vogt · 2023 · Angewandte Chemie International Edition
- Bacillus thuringiensis Cry1Da_7 and Cry1B.868 Protein Interactions with Novel Receptors Allow Control of Resistant Fall Armyworms, Spodoptera frugiperda (J.E. Smith)Yanfei Wang, Jinling Wang, Xiaoran Fu, Jeffrey R. Nageotte, Jennifer Silverman, Eric C. Bretsnyder, Danqi Chen, Timothy J. Rydel, Gregory J. Bean, Ke Sherry Li et al. · 2019 · Applied and Environmental Microbiology
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- Multiplexed imaging mass spectrometry of the extracellular matrix using serial enzyme digests from formalin-fixed paraffin-embedded tissue sectionsCassandra L. Clift, Richard R. Drake, Anand S. Mehta, Peggi M. Angel · 2020 · Analytical and Bioanalytical Chemistry
- Innovations in CAZyme gene diversity and its modification for biorefinery applicationsDixita Chettri, Ashwani Kumar Verma, Anil Kumar Verma · 2020 · Biotechnology Reports
- Dynamic ProteomicsW.E. Holmes, Thomas E. Angel, K.W. Li, M K Hellerstein · 2015 · Methods in enzymology on CD-ROM/Methods in enzymology
- Proteomics and peptidomics: moving toward precision medicine in urological malignanciesAshley Di Meo, Maria Diamandis Pasic, George Makram Yousef · 2016 · Oncotarget
- Lipid–oligonucleotide conjugates for bioapplicationsXiaowei Li, Kejun Feng, Long Li, Lu Yang, Xiaoshu Pan, Hoda Safari Yazd, Cheng Cui, Juan Li, Leonid L. Moroz, Yujia Sun et al. · 2020 · National Science Review
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- Current Methods of Post-Translational Modification Analysis and Their Applications in Blood CancersKatie Dunphy, Paul Dowling, Despina Bazou, Peter O’Gorman · 2021 · Cancers
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- Glycoprotein Enrichment Analytical TechniquesR. Zhu, Lauren G. Zacharias, Kerry M. Wooding, Wenjing Peng, Yehia S. Mechref · 2017 · Methods in enzymology on CD-ROM/Methods in enzymology
- Assessment of Sample Preparation Bias in Mass Spectrometry-Based ProteomicsFrank Klont, Linda Bras, Justina Clarinda Wolters, Sara Ongay, Rainer Bischoff, Gyorgy Bela Halmos, Peter L. Horvatovich · 2018 · Analytical Chemistry
- Selenium-Encoded Isotopic Signature Targeted ProfilingJinjun Gao, Fan Yang, Jin−Teng Che, Yu Han, Yankun Wang, Nan Chen, Daniel W. Bak, Shuchang Lai, Xiao Xie, Eranthie Weerapana et al. · 2018 · ACS Central Science
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- Sample Clean‐up Strategies for ESI Mass Spectrometry Applications in Bottom‐up Proteomics: Trends from 2012 to 2016Ria Marni Tubaon, Paul R. Haddad, Joselito P. Quirino · 2017 · PROTEOMICS
- High sensitivity top–down proteomics captures single muscle cell heterogeneity in large proteoformsJake A. Melby, Kyle A. Brown, Zachery R. Gregorich, David S. Roberts, Emily A. Chapman, Lauren E. Ehlers, Zhan Gao, Eli J. Larson, Yutong Jin, Justin R. Lopez et al. · 2023 · Proceedings of the National Academy of Sciences
- Recent developments and applications of capillary and microchip electrophoresis in proteomic and peptidomic analysesSille Štěpánová, Václav Kašička · 2015 · Journal of Separation Science
- The secretome of skeletal muscle cells: A systematic reviewAntoine Florin, Cécile Lambert, Christelle Sanchez, Jérémie Zappia, Nancy Durieux, Antonio Martins Tieppo, Ali Mobasheri, Yves Edgard Henrotin · 2020 · Osteoarthritis and Cartilage Open
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- Oxidative Modification of Proteins: From Damage to Catalysis, Signaling, and BeyondMarilene Demasi, Ohára Augusto, Etelvino José Henriques Bechara, Renata Naporano Bicev, Fernanda M. Cerqueira, Fernanda Marques da Cunha, Ana Denicola, Fernando Gomes, Sayuri Miyamoto, Luís Eduardo Soares Netto et al. · 2021 · Antioxidants and Redox Signaling
- The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometryKirk W. Gaston, Patrick A. Limbach · 2014 · RNA Biology
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- Peptidomic analyses: The progress in enrichment and identification of endogenous peptidesJiaxi Peng, Hongyan Zhang, Huan Niu, Ren’an Wu · 2020 · TrAC Trends in Analytical Chemistry
- Automated proteomic sample preparation: The key component for high throughput and quantitative mass spectrometry analysisQin Fu, Christopher I. Murray, Oleg A. Karpov, Jennifer E. Van Eyk · 2021 · Mass Spectrometry Reviews
- Studying protein structure and function by native separation–mass spectrometryGuusje van Schaick, Rob Haselberg, Govert W. Somsen, Manfred Wuhrer, Elena Domínguez‐Vega · 2022 · Nature Reviews Chemistry
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- Bottom-Up Proteomics (2013–2015): Keeping up in the Era of Systems BiologyJanice Mayne, Zhibin Ning, Xu Zhang, Amanda E. Starr, Rui Chen, Shelley A. Deeke, Cheng‐Kang Chiang, Bo Xu, Ming Wen, Kai Cheng et al. · 2015 · Analytical Chemistry
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- Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signalingKauko, Otto, Laajala, Teemu Daniel, Jumppanen, Mikael, Hintsanen, Petteri, Suni, Veronika, Haapaniemi, Pekka, Corthals, Garry, Aittokallio, Tero, Westermarck, Jukka, Imanishi, Susumu Y. · 2015 · Scientific Reports
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- Affinity Proteomics to Study Endogenous Protein Complexes: Pointers, Pitfalls, Preferences and PerspectivesJohn LaCava, Kelly R. Molloy, Martin S. Taylor, Michal Domanski, Brian T. Chait, Michael P. Rout · 2015 · BioTechniques
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