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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- Enzyme and Chemical Assisted N-Terminal Blocked Peptides Analysis, ENCHANT, as a Selective Proteomics Approach Complementary to Conventional Shotgun ApproachJingnan Huang, Jie Wang, Qingqing Li, Yang Zhang, Xumin Zhang · 2017 · Journal of Proteome Research
- Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted ProteomicsGhaith M. Hamza, Vladislav B. Bergo, Sergey V. Mamaev, Don M. Wojchowski, Paul T. Toran, Camilla R. Worsfold, Maria Paola Castaldi, Jeffrey C. Silva · 2020 · International Journal of Molecular Sciences
- Improving the performance of proteomic analysis via VAILase cleavage and 193-nm ultraviolet photodissociationBinwen Sun, Zheyi Liu, Xiang Fang, Xiaolei Wang, Can Lai, Lin Liu, Chunlei Xiao, You Jiang, Fangjun Wang · 2021 · Analytica Chimica Acta
- MaCPepDB: A Database to Quickly Access All Tryptic Peptides of the UniProtKBJulian Uszkoreit, Dirk Winkelhardt, Katalin Barkovits, Maximilian Wulf, Sascha Roocke, Katrin Marcus, Martin Eisenacher · 2021 · Journal of Proteome Research
- Multiplexed Conformationally Selective, Localized Gas-Phase Hydrogen Deuterium Exchange of Protein Ions Enabled by Transmission-Mode Electron Capture DissociationRitu Chaturvedi, Ian Webb · 2022 · Analytical Chemistry
- Structural Investigation of Therapeutic Antibodies Using Hydroxyl Radical Protein Footprinting MethodsCorie Y. Ralston, Joshua S. Sharp · 2022 · Antibodies
- Metalloenzymes play major roles to achieve high-rate nitrogen removal in N-damo communities: Lessons from metaproteomicsSilvana Quiton-Tapia, Alba Trueba-Santiso, Juan Manuel Garrido, Sonia Suárez, F. Omil · 2023 · Bioresource Technology
- Multiomics for Crop ImprovementPalak Chaturvedi, Iro Pierides, Shuang Zhang, Jana Schwarzerová, Arindam Ghatak, Wolfram Weckwerth · 2024 · Sustainability Sciences in Asia and Africa
- Cancer proteomics: developments in technology, clinical use and commercializationNai Chien Yeat, Charlotte Lin, Monica Sager, Jimmy Lin · 2015 · Expert Review of Proteomics
- Improved tryptic digestion assisted with an acid-labile anionic surfactant for the separation and characterization of glycopeptide glycoforms of a proteolytic-resistant glycoprotein by capillary electrophoresis time-of-flight mass spectrometryAlbert Barroso, Estela Giménez, Fernando Benavente, José Barbosa, Victòria Sanz‐Nebot · 2015 · Electrophoresis
- Glycoproteins Enrichment and LC-MS/MS Glycoproteomics in Central Nervous System ApplicationsRui Zhu, Ehwang Song, Ahmed Hussein, Firas H. Kobeissy, Yehia S. Mechref · 2017 · Methods in molecular biology
- Integrated omics approaches to characterize a nuclear receptor corepressor-associated histone deacetylase in mouse skeletal muscleYingyun Gong, Rui Cao, Guolian Ding, Sungguan Hong, Wenjun Zhou, Wenyun Lu, Manashree Damle, Bin Fang, Chuhan Wang, Justin Qian et al. · 2017 · Molecular and Cellular Endocrinology
- A Combination of Histological, Physiological, and Proteomic Approaches Shed Light on Seed Desiccation Tolerance of the Basal Angiosperm Amborella trichopodaMatthieu Villegente, Philippe Marmey, Claudette Job, Marc Galland, Gwendal Cueff, Béatrice Godin, Loïc Rajjou, Thierry Balliau, Michel Zivy, Bruno Fogliani et al. · 2017 · Proteomes
- Influence of NanoLC Column and Gradient Length as well as MS/MS Frequency and Sample Complexity on Shotgun Protein Identification of Marine BacteriaLars Wöhlbrand, Ralf Rabus, Bernd Blasius, Christoph Feenders · 2017 · Microbial Physiology
- Integrating Carbamylation and Ultraviolet Photodissociation Mass Spectrometry for Middle-Down ProteomicsJames D. Sanders, Sylvester M. Greer, Jennifer S. Brodbelt · 2017 · Analytical Chemistry
- Phosphopeptide Enrichment Coupled with Label-free Quantitative Mass Spectrometry to Investigate the Phosphoproteome in Prostate CancerLarry C. Cheng, Zhen Li, Thomas G. Graeber, Nicholas Alexander Graham, Justin M. Drake · 2018 · Journal of Visualized Experiments
- Exploring the Rampant Expansion of Ubiquitin ProteomicsAmalia Rose, Thibault Mayor · 2018 · Methods in molecular biology
- Using proteomics for an insight into the performance of activated sludge in a lab-scale WWTPAsma Azizan, Farnusch Kaschani, Hellen Barinas, Svenja Blaskowski, Markus Kaiser, Martin Denecke · 2020 · International Biodeterioration & Biodegradation
- Selective Maleylation-Directed Isobaric Peptide Termini Labeling for Accurate Proteome QuantificationXiaobo Tian, Marcel P. de Vries, Susan W. J. Visscher, Hjalmar P. Permentier, Rainer Bischoff · 2020 · Analytical Chemistry
- Surfactant-Induced Artifacts during Proteomic Sample PreparationYuhuan Ji, Minjing Liu, Markus Michael Bachschmid, Catherine E. Costello, Cheng Lin · 2015 · Analytical Chemistry
- Mass Spectrometry-Based Proteomics for Seafood Allergen Detection and Quantification: Current Trends and Technological FrontiersManuel G. Amado, Manuel Pazos, Mónica Carrera · 2025 · International Journal of Molecular Sciences
- Atomistic Details of Peptide Reversed-Phase Liquid Chromatography from Molecular Dynamics SimulationsPablo M. Scrosati, Lars Konermann · 2023 · Analytical Chemistry
- Top-Down Analysis of Supercharged Proteins Using Collision-, Electron-, and Photon-Based Activation MethodsKyle J. Juetten, Jennifer S. Brodbelt · 2023 · Journal of the American Society for Mass Spectrometry
- Characterizing citrullination by mass spectrometry-based proteomicsAlexandra K.L.F.S. Rebak, Ivo Alexander Hendriks, Michael Lund Nielsen · 2023 · Philosophical Transactions of the Royal Society B Biological Sciences
- Biotechnological Potential of Macroalgae during Seasonal Blooms for Sustainable Production of UV-Absorbing CompoundsNedeljka N. Rosic, Carol Thornber · 2023 · Marine Drugs
- Environmental proteomics as a useful methodology for early-stage detection of stress in anammox engineered systemsVíctor Guzmán‐Fierro, Alberto Dieguez-Seoane, Marlene Roeckel, Juan Manuel Lema, Alba Trueba-Santiso · 2023 · The Science of The Total Environment
- [Cu2(trz-ia)2]─An Ultramicroporous Cu2 Paddle Wheel Triazolyl Isophthalate MOF: A Comparative Study of Its Properties in Dihydrogen Adsorption and Isotopologue SeparationSibo Chetry, Prantik Sarkar, Volodymyr Bon, Muhammad Fernadi Lukman, Andreas Pöppl, Michael Hirscher, Stefan Kaskel, Harald Krautscheid · 2025 · Inorganic Chemistry
- Proteomic analysis of cell fate decisionJenny Hansson, Jeroen Krijgsveld · 2013 · Current Opinion in Genetics & Development
- Snake Venom Proteopeptidomics: What Lies Behind the CurtainRichard Hemmi Valente, Carolina Alves Nicolau, Jonás Perales, Ana Gisele C. Neves‐Ferreira · 2016 · Springer eBooks
- A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomicsJane I. Khudyakov, Jared S. Deyarmin, Ryan Matthew Hekman, Laura Pujade Busqueta, Rasool Maan, Melony Mody, Reeti Banerjee, Daniel E. Crocker, Cory D. Champagne · 2018 · Biology Open
- MiTPeptideDB: a proteogenomic resource for the discovery of novel peptidesElizabeth Guruceaga, Alba Garín-Muga, Víctor Segura · 2019 · Bioinformatics
- GLOBAL AND TARGETED PROFILING OF GTP‐BINDING PROTEINS IN BIOLOGICAL SAMPLES BY MASS SPECTROMETRYMing Huang, Yinsheng Wang · 2020 · Mass Spectrometry Reviews
- Mapping the plant proteome: tools for surveying coordinating pathwaysAmanda L. Smythers, Leslie M. Hicks · 2021 · Emerging Topics in Life Sciences
- Integrative network analysis reveals USP7 haploinsufficiency inhibits E-protein activity in pediatric T-lineage acute lymphoblastic leukemia (T-ALL)Timothy I. Shaw, Li Dong, Liqing Tian, Chenxi Qian, Yu Liu, Bensheng Ju, Anthony A. High, Kanisha Kavdia, Vishwajeeth Pagala, Bridget Shaner et al. · 2021 · Scientific Reports
- Microproteins: from behind the scenes to the spotlightMeiqian Jiang, Huiqiang Lou, Wenya Hou · 2021 · Genome Instability & Disease
- Proteomics with Enhanced In-Source Fragmentation/Annotation: Applying XCMS-EISA Informatics and Q-MRM High-Sensitivity QuantificationJingchuan Xue, Rico J. E. Derks, Linh T. Hoang, Martin A. Giera, Gary E. Siuzdak · 2021 · Journal of the American Society for Mass Spectrometry
- Preparative capillary electrophoresis (CE) fractionation of protein digests improves protein and peptide identification in bottom-up proteomicsSimon D. Weaver, Naviya Schuster-Little, Rebecca J. Whelan · 2022 · Analytical Methods
- Hyperplexing Approaches for up to 45-Plex Quantitative Proteomic AnalysisZhen Wu, Weirong Xiang, Lin Huang, Shuwei Li, Xumin Zhang · 2023 · Analytical Chemistry
- Combining offline high performance liquid chromatography fractionation of peptides and intact proteins to enhance proteome coverage in bottom-up proteomicsLeena M. Patil, David H. Parkinson, Nathan R. Zuniga, Hsien‐Jung L. Lin, Bradley C. Naylor, John C. Price · 2022 · Journal of Chromatography A
- In SilicoProteome Cleavage Reveals Iterative Digestion Strategy for High Sequence CoverageJesse G. Meyer · 2014 · ISRN Computational Biology
- Designing biomedical proteomics experiments: state-of-the-art and future perspectivesEvelyne Maes, Pieter Kelchtermans, Wout Bittremieux, Kurt De Grave, Sven Degroeve, Jef Hooyberghs, Inge Mertens, Geert Baggerman, Jan Ramon, Kris Laukens et al. · 2016 · Expert Review of Proteomics
- High-throughput proteomics and the fight against pathogensAnita Horvatić, Josipa Kuleš, Nicolas Guillemin, Asier Galán, Vladimir Mrljak, Mangesh Ramesh Bhide · 2016 · Molecular BioSystems
- Proteomic analysis of Aspergillus fumigatus – clinical implicationsNicola M. Moloney, Rebecca A. Owens, Seán Doyle · 2016 · Expert Review of Proteomics
- Protein turnover measurement using selected reaction monitoring-mass spectrometry (SRM-MS)Stephen W. Holman, Dean E. Hammond, Deborah M. Simpson, John Waters, Jane L. Hurst, Robert Jeffrey Beynon · 2016 · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences
- Do the complementarities of electrokinetic and chromatographic procedures represent the “Swiss knife” in proteomic investigation? An overview of the literature in the past decadeMonica Di Venere, Simona Viglio, Davide Sassera, Marco Fumagalli, Anna Bardoni, Roberta Salvini, Maddalena Cagnone, Paolo Iadarola · 2017 · Electrophoresis
- Human Exoproteome in Acute Apical AbscessesCristiane Ferreira Alfenas, Tiago Antônio de Oliveira Mendes, Humberto Josué de Oliveira Ramos, Fernanda Prieto Bruckner, HS Antunes, Isabela Neves Rôças, José Freitas Siqueira Jr, José Claudio Provenzano · 2017 · Journal of Endodontics
- Enhanced protein identification using graphite-modified MALDI plates for offline LC-MALDI-MS/MS bottom-up proteomicsAnthony D. Maus, Rudolph Mignon, Franco Basile · 2018 · Analytical Biochemistry
- FractionOptimizer: a method for optimal peptide fractionation in bottom-up proteomicsElizaveta M. Solovyeva, Anna A. Lobas, Arthur Tigranovich Kopylov, Irina Y. Ilina, Lev I. Levitsky, Sergei A. Moshkovskii, Mikhail V. Gorshkov · 2018 · Analytical and Bioanalytical Chemistry
- Recent Advances in MS-Based Plant Proteomics: Proteomics Data Validation Through Integration with Other Classic and -Omics ApproachesMaría-Dolores Rey, Luís Valledor, María Ángeles Castillejo, Rosa Sánchez‐Lucas, Cristina López‐Hidalgo, Víctor M. Guerrero-Sánchez, Francisco Colina, Monica Escandón, Ana María Maldonado-Alconada, Jesús Valentín Jorrín-Novo · 2019 · Progress in botany
- Proteomics of Select Neglected Tropical DiseasesAnthony J. Saviola, Fernanda Novelli Negrão, John R. Yates · 2020 · Annual Review of Analytical Chemistry
- Molecular Surgery: Proteomics of a Rare Genetic Disease Gives Insight into Common Causes of BlindnessGabriel Velez, Vinit B. Mahajan · 2020 · iScience
- Mapping Complex Disulfide Bonds via Implementing Photochemical Reduction Online with Liquid Chromatography–Mass SpectrometryXiaoyue Yang, Yu Xia · 2020 · Journal of the American Society for Mass Spectrometry
- Comparative Proteomic Analysis to Investigate the Pathogenesis of Oral Adenoid Cystic CarcinomaWen Li, Qian Zhang, Xiaobin Wang, Hanlin Wang, Wenxin Zuo, Hongliang Xie, Jianming Tang, Mengmeng Wang, Zhipeng Zeng, Wanxia Cai et al. · 2021 · ACS Omega
- Sample Preparation Matters for Peptide Mapping to Evaluate Deamidation of Adeno-Associated Virus Capsid Proteins Using Liquid Chromatography–Tandem Mass SpectrometryYu Zhou, Yueju Wang · 2022 · Human Gene Therapy
- Advances in proteomics for production strain analysisAndrew R. Landels, Caroline A. Evans, Josselin Noirel, Phillip Craig Wright · 2015 · Current Opinion in Biotechnology
- Gas-phase acid-base properties of homocysteine, homoserine, 5-mercaptonorvaline, and 5-hydroxynorvaline from the extended kinetic methodCorbin E. Muetterties, Ashley Janiga, Kathy T. Huynh, M. Grace Pisano, Valerie T. Tripp, Douglas D. Young, John C. Poutsma · 2014 · International Journal of Mass Spectrometry
- Label-free protein quantification after ultrafast digestion of complex proteomes using ultrasonic energy and immobilized-trypsin magnetic nanoparticlesGonçalo Martins, Javier Fernández‐Lodeiro, Jamila Djafari, Carlos Lodeiro, José Luís Capelo, Hugo Miguel Santos · 2018 · Talanta
- Degronomics: Mapping the Interacting Peptidome of a Ubiquitin Ligase Using an Integrative Mass Spectrometry StrategyCanzani, Daniele, Rusnac, Domniţa-Valeria, Zheng, Ning, Bush, Matthew F. · 2019 · Analytical Chemistry
- Chemical and linguistic considerations for encoding Chinese characters: an embodiment using chain-end degradable sequence-defined oligourethanes created by consecutive solid phase click chemistryLe Zhang, Todd B. Krause, Harnimarta Deol, Bipin Pandey, Qifan Xiao, Hyun Meen Park, Brent L. Iverson, Danny Law, Eric V. Anslyn · 2024 · Chemical Science
- Mass spectrometry based proteomics: Changing the impact of protein analysis in forensic scienceRomy E. Keane, Rebecca J. Tidy, Glendon J. Parker, Joel P. A. Gummer, Colin Priddis · 2024 · Wiley Interdisciplinary Reviews Forensic Science
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- In Situ Metal–Organic Framework Growth in Serum Encapsulates and Depletes Abundant Proteins for Integrated Plasma ProteomicsEmily A. Reasoner, Hsin‐Ju Chan, Timothy J. Aballo, Kylie Plouff, Seungwoo Noh, Ying Ge, Song Jin · 2025 · ACS Nano
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- Controllable construction of Titanium dioxide-Zirconium dioxide@Zinc hydroxyfluoride networks in micro-capillaries for bio-analysisGang Wang, Zhongyuan He, Guoying Shi, Hongzhi Wang, Qinghong Zhang, Yaogang Li · 2015 · Journal of Colloid and Interface Science
- Direct digestion of proteins in living cells into peptides for proteomic analysisQi Chen, Guoquan Yan, Mingxia Gao, Xiangmin Zhang · 2014 · Analytical and Bioanalytical Chemistry
- Human-Derived Brain Models: Windows into Neuropsychiatric Disorders and Drug TherapiesAlexis R. Papariello, Karen Litwa · 2019 · Assay and Drug Development Technologies
- Evaluation of Sibling and Twin Fragment Ions Improves the Structural Characterization of Proteins by Top-Down MALDI In-Source Decay Mass SpectrometrySimone Nicolardi, David P. A. Kilgour, Natasja Dolezal, Jan Wouter Drijfhout, Manfred Wuhrer, Yuri E. M. van der Burgt · 2020 · Analytical Chemistry
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- Automated Proteomics Workflows for High-Throughput Library Generation and Biomarker Detection Using Data-Independent AcquisitionSelvam Paramasivan, Janna Leigh Morrison, Mitchell C. Lock, Jack R. T. Darby, Roberto A. Barrero, Paul Christian Mills, Pawel G. Sadowski · 2023 · Journal of Proteome Research
- Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometrySimone Sidoli, Rina Fujiwara, Katarzyna Kulej, Benjamin Aaron Garcia · 2016 · Molecular BioSystems
- The Schistosomiasis SpleenOME: Unveiling the Proteomic Landscape of Splenomegaly Using Label-Free Mass SpectrometryMiguel Cosenza‐Contreras, Renata Alves de Oliveira e Castro, Bruno Mattei, Jonatan Marques Campos, Gustavo Gonçalves Silva, Nívia Carolina Nogueira de Paiva, Rodrigo Dian de Oliveira Aguiar‐Soares, Cláudia Martins Carneiro, Luís Afonso, William Castro‐Borges · 2019 · Frontiers in Immunology
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- Next-Generation Sequencing for Venomics: Application of Multi-Enzymatic Limited Digestion for Inventorying the Snake Venom ArsenalFernanda Gobbi Amorim, Damien Redureau, Thomas Crasset, Lou Freuville, Dominique Baiwir, Gabriel Mazzucchelli, Stefanie K. Menzies, Nicholas R. Casewell, Loïc Quinton · 2023 · Toxins
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- Current Insights on the Impact of Proteomics in Respiratory AllergiesJuan Carlos Vizuet‐de‐Rueda, Josaphat Miguel Montero‐Vargas, Miguel Ángel Galván-Morales, Raúl Porras‐Gutiérrez‐de‐Velasco, Luis Manuel Teran · 2022 · International Journal of Molecular Sciences
- Liquid chromatography coupled to tandem mass spectrometry for comprehensive quantification of crustacean tropomyosin and arginine kinase in food matrixHuan Li, Tianshu Li, Yanbo Wang, Shuifeng Zhang, Huadong Sheng, Linglin Fu · 2022 · Food Control
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- Brain Proteome Changes Induced by Olfactory Learning inDrosophilaYaoyang Zhang, Bing Shan, Monica Boyle, Jacqueline Liu, Lujian Liao, Tao Xu, John R. Yates · 2014 · Journal of Proteome Research
- Shotgun Quantitative Proteomic Analysis of Proteins Responding to Drought Stress inBrassica rapaL. (Inbred Line “Chiifu”)Soon‐Wook Kwon, Mijeong Kim, Hijin Kim, Joohyun Lee · 2016 · International Journal of Genomics