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Citations	Article
59	Multi-Omics Integration for the Design of Novel Therapies and the Identification of Novel Biomarkers by Tonci Ivanisevic and Raj N. Sewduth
43	Transforming Clinical Research: The Power of High-Throughput Omics Integration by Rui Vitorino
32	Salivary Biomarkers in Oral Squamous Cell Carcinoma: A Proteomic Overview by Gabriele Riccardi, Mario Giuseppe Bellizzi, Irene Fatuzzo, Federica Zoccali, Luca Cavalcanti, Antonio Greco, Marco de Vincentiis, Massimo Ralli, Marco Fiore, Carla Petrella, Antonio Minni and Christian Barbato
22	Post-Translational Modifications in Histones and Their Role in Abiotic Stress Tolerance in Plants by Madhvi Sharma, Amanpreet K. Sidhu, Mahesh Kumar Samota, Mamta Gupta, Pushpendra Koli and Mukesh Choudhary
20	Proteomics-Based Identification of Dysregulated Proteins in Breast Cancer by Anca-Narcisa Neagu, Madhuri Jayathirtha, Danielle Whitham, Panashe Mutsengi, Isabelle Sullivan, Brindusa Alina Petre and Costel C. Darie
16	Biomarkers in Ovarian Cancer: Towards Personalized Medicine by Carlos López-Portugués, María Montes-Bayón and Paula Díez
15	Proteomics-Based Identification of Dysregulated Proteins and Biomarker Discovery in Invasive Ductal Carcinoma, the Most Common Breast Cancer Subtype by Anca-Narcisa Neagu, Danielle Whitham, Logan Seymour, Norman Haaker, Isabella Pelkey and Costel C. Darie
14	Algorithmically Reconstructed Molecular Pathways as the New Generation of Prognostic Molecular Biomarkers in Human Solid Cancers by Marianna Zolotovskaia, Maks Kovalenko, Polina Pugacheva, Victor Tkachev, Alexander Simonov, Maxim Sorokin, Alexander Seryakov, Andrew Garazha, Nurshat Gaifullin, Marina Sekacheva, Galina Zakharova and Anton A. Buzdin
12	Anti-Cancer Properties of Flaxseed Proteome by Yulia Merkher, Elizaveta Kontareva, Anastasia Alexandrova, Rajesha Javaraiah, Margarita Pustovalova and Sergey Leonov
12	The Need for Biomarkers in the ALS–FTD Spectrum: A Clinical Point of View on the Role of Proteomics by Francesca Vignaroli, Angelica Mele, Giacomo Tondo, Veronica De Giorgis, Marcello Manfredi, Cristoforo Comi, Letizia Mazzini and Fabiola De Marchi

Citations	Article
59	Multi-Omics Integration for the Design of Novel Therapies and the Identification of Novel Biomarkers by Tonci Ivanisevic and Raj N. Sewduth
43	Transforming Clinical Research: The Power of High-Throughput Omics Integration by Rui Vitorino
22	Post-Translational Modifications in Histones and Their Role in Abiotic Stress Tolerance in Plants by Madhvi Sharma, Amanpreet K. Sidhu, Mahesh Kumar Samota, Mamta Gupta, Pushpendra Koli and Mukesh Choudhary
16	Biomarkers in Ovarian Cancer: Towards Personalized Medicine by Carlos López-Portugués, María Montes-Bayón and Paula Díez
12	Anti-Cancer Properties of Flaxseed Proteome by Yulia Merkher, Elizaveta Kontareva, Anastasia Alexandrova, Rajesha Javaraiah, Margarita Pustovalova and Sergey Leonov
11	Benefits of FAIMS to Improve the Proteome Coverage of Deteriorated and/or Cross-Linked TMT 10-Plex FFPE Tissue and Plasma-Derived Exosomes Samples by Ana Montero-Calle, María Garranzo-Asensio, Raquel Rejas-González, Jaime Feliu, Marta Mendiola, Alberto Peláez-García and Rodrigo Barderas
9	Proteomics—The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience by Jens R. Coorssen and Matthew P. Padula
8	*Comparison of the Proteomes and Phosphoproteomes of S. cerevisiae* Cells Harvested with Different Strategies by Valentina Rossio and Joao A. Paulo**
7	Unveiling the Molecular Footprint: Proteome-Based Biomarkers for Alzheimer’s Disease by Mukul Jain, Rupal Dhariwal, Nil Patil, Sandhya Ojha, Reshma Tendulkar, Mugdha Tendulkar, Parmdeep Singh Dhanda, Alpa Yadav and Prashant Kaushik
6	The Mechanisms of Regulated Cell Death: Structural and Functional Proteomic Pathways Induced or Inhibited by a Specific Protein—A Narrative Review by Diego Fernández-Lázaro, Begoña Sanz and Jesús Seco-Calvo

Citations	Article
43	Transforming Clinical Research: The Power of High-Throughput Omics Integration by Rui Vitorino
4	Proteomics of Extracellular Vesicles: Recent Updates, Challenges and Limitations by Mohini Singh, Prashant Kumar Tiwari, Vivek Kashyap and Sanjay Kumar
3	Circulating Factors as Potential Biomarkers of Cardiovascular Damage Progression Associated with Type 2 Diabetes by Giovanni Sartore, Francesco Piarulli, Eugenio Ragazzi, Alice Mallia, Stefania Ghilardi, Massimo Carollo, Annunziata Lapolla and Cristina Banfi
3	DNA Damage-Induced Ferroptosis: A Boolean Model Regulating p53 and Non-Coding RNAs in Drug Resistance by Shantanu Gupta, Daner A. Silveira, José Carlos M. Mombach and Ronaldo F. Hashimoto
3	Proteomic Comparison of Acute Myeloid Leukemia Cells and Normal CD34⁺ Bone Marrow Cells: Studies of Leukemia Cell Differentiation and Regulation of Iron Metabolism/Ferroptosis by Frode Selheim, Elise Aasebø, Håkon Reikvam, Øystein Bruserud and Maria Hernandez-Valladares
2	Towards Characterization of Hass Avocado Peel and Pulp Proteome during Postharvest Shelf Life by Carolina Camacho-Vázquez, José Miguel Elizalde-Contreras, Francisco Antonio Reyes-Soria, Juan Luis Monribot-Villanueva, José Antonio Guerrero-Analco, Janet Juarez-Escobar, Olinda Velázquez-López, Thuluz Meza-Menchaca, Esaú Bojórquez-Velázquez, Jesús Alejandro Zamora-Briseño, Monica Ramirez-Vazquez, Guadalupe Alheli González Barrenechea, Enrique Ibarra-Laclette and Eliel Ruiz-May
2	Transcriptomics Revealed Differentially Expressed Transcription Factors and MicroRNAs in Human Diabetic Foot Ulcers by Vikrant Rai
2	Phospho-Proteomics Analysis of Early Response to X-Ray Irradiation Reveals Molecular Mechanism Potentially Related to U251 Cell Radioresistance by Ousseynou Ben Diouf, Antoine Gilbert, Benoit Bernay, Randi G. Syljuåsen, Mihaela Tudor, Mihaela Temelie, Diana I. Savu, Mamadou Soumboundou, Cheikh Sall and François Chevalier
2	Structure-Based Deep Learning Framework for Modeling Human–Gut Bacterial Protein Interactions by Despoina P. Kiouri, Georgios C. Batsis and Christos T. Chasapis
1	Novel Integration of Spatial and Single-Cell Omics Data Sets Enables Deeper Insights into IPF Pathogenesis by Fei Wang, Liang Jin, Xue Wang, Baoliang Cui, Yingli Yang, Lori Duggan, Annette Schwartz Sterman, Sarah M. Lloyd, Lisa A. Hazelwood, Neha Chaudhary, Bhupinder Bawa, Lucy A. Phillips, Yupeng He and Yu Tian

Citations	Article
4	Proteomics of Extracellular Vesicles: Recent Updates, Challenges and Limitations by Mohini Singh, Prashant Kumar Tiwari, Vivek Kashyap and Sanjay Kumar
1	Cell-Type-Specific Heat-Induced Changes in the Proteomes of Pollen Mother Cells and Microspores Provide New Insights into Tomato Pollen Production Under Elevated Temperature by Priya Thapa, Jun Guo, Kajol Pradhan, Dibya Thapa, Sudhakar Madhavarapu, Jing Zou, Jesse Potts, Hui Li, Joshua O’Hair, Chen Wang, Suping Zhou, Yong Yang, Tara Fish and Theodore W. Thannhauser
1	Intrinsic Disorder and Phase Separation Coordinate Exocytosis, Motility, and Chromatin Remodeling in the Human Acrosomal Proteome by Shivam Shukla, Sean S. Lastorka and Vladimir N. Uversky
1	Oxidative Stress and Its Role in the Emergence and Progression of Myelodysplastic Syndromes: Insights from Proteomic Analysis and Other Methodologies by Anastasia Boura-Theodorou, Konstantina Psatha, Stefania Maniatsi, Areti Kourti, Georgia Kaiafa, Michalis Aivaliotis and Kali Makedou
1	Proteomic Profiling Reveals Novel Molecular Insights into Dysregulated Proteins in Established Cases of Rheumatoid Arthritis by Afshan Masood, Hicham Benabdelkamel, Assim A. Alfadda, Abdurhman S. Alarfaj, Amina Fallata, Salini Scaria Joy, Maha Al Mogren, Anas M. Abdel Rahman and Mohamed Siaj

Citations	Article
248	A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field by Emmalyn J. Dupree, Madhuri Jayathirtha, Hannah Yorkey, Marius Mihasan, Brindusa Alina Petre and Costel C. Darie
189	Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics by Benjamin C. Orsburn
153	“Omics”-Informed Drug and Biomarker Discovery: Opportunities, Challenges and Future Perspectives by Holly Matthews, James Hanison and Niroshini Nirmalan
127	Milk-Derived Extracellular Vesicles in Inter-Organism, Cross-Species Communication and Drug Delivery by Rahul Sanwlani, Pamali Fonseka, Sai V. Chitti and Suresh Mathivanan
126	Transcription Factor Functional Protein-Protein Interactions in Plant Defense Responses by Murilo S. Alves, Silvana P. Dadalto, Amanda B. Gonçalves, Gilza B. De Souza, Vanessa A. Barros and Luciano G. Fietto
121	Personalized Proteomics: The Future of Precision Medicine by Trevor T. Duarte and Charles T. Spencer
103	Applications of Proteomics in Ovarian Cancer: Dawn of a New Era by Aruni Ghose, Sri Vidya Niharika Gullapalli, Naila Chohan, Anita Bolina, Michele Moschetta, Elie Rassy and Stergios Boussios
87	Isoelectric Point Separations of Peptides and Proteins by Melissa R. Pergande and Stephanie M. Cologna
79	Proteomes Are of Proteoforms: Embracing the Complexity by Katrina Carbonara, Martin Andonovski and Jens R. Coorssen
77	Proteome Profiling of Exosomes Purified from a Small Amount of Human Serum: The Problem of Co-Purified Serum Components by Mateusz Smolarz, Monika Pietrowska, Natalia Matysiak, Łukasz Mielańczyk and Piotr Widłak

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7553	Optimization of a Protocol for Protein Extraction from Calcified Aortic Valves for Proteomics Applications: Development of a Standard Operating Procedure by Fábio Trindade, Ana F. Ferreira, Francisca Saraiva, Diana Martins, Vera M. Mendes, Carla Sousa, Cristina Gavina, Adelino Leite-Moreira, Bruno Manadas, Inês Falcão-Pires and Rui Vitorino
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6062	Salivary Biomarkers in Oral Squamous Cell Carcinoma: A Proteomic Overview by Gabriele Riccardi, Mario Giuseppe Bellizzi, Irene Fatuzzo, Federica Zoccali, Luca Cavalcanti, Antonio Greco, Marco de Vincentiis, Massimo Ralli, Marco Fiore, Carla Petrella, Antonio Minni and Christian Barbato
5923	Proteomics-Based Identification of Dysregulated Proteins and Biomarker Discovery in Invasive Ductal Carcinoma, the Most Common Breast Cancer Subtype by Anca-Narcisa Neagu, Danielle Whitham, Logan Seymour, Norman Haaker, Isabella Pelkey and Costel C. Darie
5736	Post-Translational Modifications in Histones and Their Role in Abiotic Stress Tolerance in Plants by Madhvi Sharma, Amanpreet K. Sidhu, Mahesh Kumar Samota, Mamta Gupta, Pushpendra Koli and Mukesh Choudhary

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10179	Multi-Omics Integration for the Design of Novel Therapies and the Identification of Novel Biomarkers by Tonci Ivanisevic and Raj N. Sewduth
8630	Transforming Clinical Research: The Power of High-Throughput Omics Integration by Rui Vitorino
8390	Biomarkers in Ovarian Cancer: Towards Personalized Medicine by Carlos López-Portugués, María Montes-Bayón and Paula Díez
5736	Post-Translational Modifications in Histones and Their Role in Abiotic Stress Tolerance in Plants by Madhvi Sharma, Amanpreet K. Sidhu, Mahesh Kumar Samota, Mamta Gupta, Pushpendra Koli and Mukesh Choudhary
5537	Unveiling the Molecular Footprint: Proteome-Based Biomarkers for Alzheimer’s Disease by Mukul Jain, Rupal Dhariwal, Nil Patil, Sandhya Ojha, Reshma Tendulkar, Mugdha Tendulkar, Parmdeep Singh Dhanda, Alpa Yadav and Prashant Kaushik
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5412	Proteomics—The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience by Jens R. Coorssen and Matthew P. Padula
5375	Plasma and Kidney Proteome Profiling Combined with Laser Capture Microdissection Reveal Large Increases in Immunoglobulins with Age by Leanne J. G. Chan, Niclas Olsson, Magdalena Preciado López, Kayley Hake, Haruna Tomono, Matthew A. Veras and Fiona E. McAllister
5272	Identification of Plasma Biomarkers from Rheumatoid Arthritis Patients Using an Optimized Sequential Window Acquisition of All THeoretical Mass Spectra (SWATH) Proteomics Workflow by Liang Jin, Fei Wang, Xue Wang, Bohdan P. Harvey, Yingtao Bi, Chenqi Hu, Baoliang Cui, Anhdao T. Darcy, John W. Maull, Ben R. Phillips, Youngjae Kim, Gary J. Jenkins, Thierry R. Sornasse and Yu Tian
5069	Anti-Cancer Properties of Flaxseed Proteome by Yulia Merkher, Elizaveta Kontareva, Anastasia Alexandrova, Rajesha Javaraiah, Margarita Pustovalova and Sergey Leonov

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4521	Protein Extraction Methods Suitable for Muscle Tissue Proteomic Analysis by Lorenza Vantaggiato, Claudia Landi, Enxhi Shaba, Daniela Rossi, Vincenzo Sorrentino and Luca Bini
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3704	DNA Damage-Induced Ferroptosis: A Boolean Model Regulating p53 and Non-Coding RNAs in Drug Resistance by Shantanu Gupta, Daner A. Silveira, José Carlos M. Mombach and Ronaldo F. Hashimoto
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2933	Multi-Omic Approaches in Cancer-Related Micropeptide Identification by Katarina Vrbnjak and Raj Nayan Sewduth
2718	Towards Characterization of Hass Avocado Peel and Pulp Proteome during Postharvest Shelf Life by Carolina Camacho-Vázquez, José Miguel Elizalde-Contreras, Francisco Antonio Reyes-Soria, Juan Luis Monribot-Villanueva, José Antonio Guerrero-Analco, Janet Juarez-Escobar, Olinda Velázquez-López, Thuluz Meza-Menchaca, Esaú Bojórquez-Velázquez, Jesús Alejandro Zamora-Briseño, Monica Ramirez-Vazquez, Guadalupe Alheli González Barrenechea, Enrique Ibarra-Laclette and Eliel Ruiz-May
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1885	Advances in the Study of Protein Deamidation: Unveiling Its Influence on Aging, Disease Progression, Forensics and Therapeutic Efficacy by Sunil S. Adav
1857	Intrinsic Disorder and Phase Separation Coordinate Exocytosis, Motility, and Chromatin Remodeling in the Human Acrosomal Proteome by Shivam Shukla, Sean S. Lastorka and Vladimir N. Uversky
1833	Next-Generation Protein–Ligand Interaction Networks: APEX as a Powerful Technology by José Miguel Quintero-Ferrer, Lucas Silva de Oliveira, Paula Marian Vieira Goulart, Thiago Albuquerque Souza Campos, Coralie Martin, Philippe Grellier, Izabela Marques Dourado Bastos and Sébastien Charneau
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4559	Anti-Cancer Properties of Flaxseed Proteome by Yulia Merkher, Elizaveta Kontareva, Anastasia Alexandrova, Rajesha Javaraiah, Margarita Pustovalova and Sergey Leonov
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1577	Post-Translational Modifications in Histones and Their Role in Abiotic Stress Tolerance in Plants by Madhvi Sharma, Amanpreet K. Sidhu, Mahesh Kumar Samota, Mamta Gupta, Pushpendra Koli and Mukesh Choudhary
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4559	Anti-Cancer Properties of Flaxseed Proteome by Yulia Merkher, Elizaveta Kontareva, Anastasia Alexandrova, Rajesha Javaraiah, Margarita Pustovalova and Sergey Leonov
2127	Multi-Omics Integration for the Design of Novel Therapies and the Identification of Novel Biomarkers by Tonci Ivanisevic and Raj N. Sewduth
1616	Biomarkers in Ovarian Cancer: Towards Personalized Medicine by Carlos López-Portugués, María Montes-Bayón and Paula Díez
1577	Post-Translational Modifications in Histones and Their Role in Abiotic Stress Tolerance in Plants by Madhvi Sharma, Amanpreet K. Sidhu, Mahesh Kumar Samota, Mamta Gupta, Pushpendra Koli and Mukesh Choudhary
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1308	Proteomics—The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience by Jens R. Coorssen and Matthew P. Padula
1296	Transforming Clinical Research: The Power of High-Throughput Omics Integration by Rui Vitorino
1127	Unveiling the Molecular Footprint: Proteome-Based Biomarkers for Alzheimer’s Disease by Mukul Jain, Rupal Dhariwal, Nil Patil, Sandhya Ojha, Reshma Tendulkar, Mugdha Tendulkar, Parmdeep Singh Dhanda, Alpa Yadav and Prashant Kaushik
1036	The Current Molecular and Cellular Landscape of Chronic Obstructive Pulmonary Disease (COPD): A Review of Therapies and Efforts towards Personalized Treatment by Luke A. Farrell, Matthew B. O’Rourke, Matthew P. Padula, Fernando Souza-Fonseca-Guimaraes, Gaetano Caramori, Peter A. B. Wark, Shymali C. Dharmage and Phillip M. Hansbro
1027	Identification of Plasma Biomarkers from Rheumatoid Arthritis Patients Using an Optimized Sequential Window Acquisition of All THeoretical Mass Spectra (SWATH) Proteomics Workflow by Liang Jin, Fei Wang, Xue Wang, Bohdan P. Harvey, Yingtao Bi, Chenqi Hu, Baoliang Cui, Anhdao T. Darcy, John W. Maull, Ben R. Phillips, Youngjae Kim, Gary J. Jenkins, Thierry R. Sornasse and Yu Tian

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1296	Transforming Clinical Research: The Power of High-Throughput Omics Integration by Rui Vitorino
930	DNA Damage-Induced Ferroptosis: A Boolean Model Regulating p53 and Non-Coding RNAs in Drug Resistance by Shantanu Gupta, Daner A. Silveira, José Carlos M. Mombach and Ronaldo F. Hashimoto
899	Novel Integration of Spatial and Single-Cell Omics Data Sets Enables Deeper Insights into IPF Pathogenesis by Fei Wang, Liang Jin, Xue Wang, Baoliang Cui, Yingli Yang, Lori Duggan, Annette Schwartz Sterman, Sarah M. Lloyd, Lisa A. Hazelwood, Neha Chaudhary, Bhupinder Bawa, Lucy A. Phillips, Yupeng He and Yu Tian
850	Assessment of Data-Independent Acquisition Mass Spectrometry (DIA-MS) for the Identification of Single Amino Acid Variants by Ivo Fierro-Monti, Klemens Fröhlich, Christian Schori and Alexander Schmidt
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782	Circulating Factors as Potential Biomarkers of Cardiovascular Damage Progression Associated with Type 2 Diabetes by Giovanni Sartore, Francesco Piarulli, Eugenio Ragazzi, Alice Mallia, Stefania Ghilardi, Massimo Carollo, Annunziata Lapolla and Cristina Banfi
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758	Proteomics of Extracellular Vesicles: Recent Updates, Challenges and Limitations by Mohini Singh, Prashant Kumar Tiwari, Vivek Kashyap and Sanjay Kumar
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15422	Isoelectric Point Separations of Peptides and Proteins by Melissa R. Pergande and Stephanie M. Cologna
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