1. “Proteomics of Extracellular Vesicles: Recent Updates, Challenges and Limitations”
by Mohini Singh, Prashant Kumar Tiwari, Vivek Kashyap and Sanjay Kumar
Proteomes 2025, 13(1), 12; https://doi.org/10.3390/proteomes13010012
Available online: https://www.mdpi.com/2227-7382/13/1/12

2. “Integrative Spatial Proteomics and Single-Cell RNA Sequencing Unveil Molecular Complexity in Rheumatoid Arthritis for Novel Therapeutic Targeting”
by Xue Wang, Fei Wang, Archana S. Iyer, Heather Knight, Lori J. Duggan, Yingli Yang, Liang Jin, Baoliang Cui, Yupeng He, Jan Schejbal et al.
Proteomes 2025, 13(2), 17; https://doi.org/10.3390/proteomes13020017
Available online: https://www.mdpi.com/2227-7382/13/2/17

3. “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 et al.
Proteomes 2025, 13(1), 3; https://doi.org/10.3390/proteomes13010003
Available online: https://www.mdpi.com/2227-7382/13/1/3

4. “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
Proteomes 2025, 13(1), 6; https://doi.org/10.3390/proteomes13010006
Available online: https://www.mdpi.com/2227-7382/13/1/6

5. “Advances in the Study of Protein Deamidation: Unveiling Its Influence on Aging, Disease Progression, Forensics and Therapeutic Efficacy”
by Sunil S. Adav
Proteomes 2025, 13(2), 24; https://doi.org/10.3390/proteomes13020024
Available online: https://www.mdpi.com/2227-7382/13/2/24

6. “In Search of Ideal Solutions for Cancer Diagnosis: From Conventional Methods to Protein Biomarkers in Liquid Biopsy”
by Anca-Narcisa Neagu, Pathea S. Bruno, Claudiu-Laurentiu Josan, Natalie Waterman, Hailey Morrissiey, Victor T. Njoku and Costel C. Darie
Proteomes 2025, 13(4), 47; https://doi.org/10.3390/proteomes13040047
Available online: https://www.mdpi.com/2227-7382/13/4/47

7. “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
Proteomes 2025, 13(3), 26; https://doi.org/10.3390/proteomes13030026
Available online: https://www.mdpi.com/2227-7382/13/3/26

8. “Comparative Analysis of Plasma Extracellular Vesicle Isolation Methods for Purity Assessment and Biomarker Discovery”
by Alexandra T. Star, Melissa Hewitt, Amanpreet Badhwar, Wen Ding, Tammy-Lynn Tremblay, Jennifer J. Hill, William G. Willmore, Jagdeep K. Sandhu and Arsalan S. Haqqani
Proteomes 2025, 13(3), 45; https://doi.org/10.3390/proteomes13030045
Available online: https://www.mdpi.com/2227-7382/13/3/45

9. “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
Proteomes 2025, 13(1), 11; https://doi.org/10.3390/proteomes13010011
Available online: https://www.mdpi.com/2227-7382/13/1/11

10. “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
Proteomes 2025, 13(2), 16; https://doi.org/10.3390/proteomes13020016
Available online: https://www.mdpi.com/2227-7382/13/2/16

11. “Deciphering Radiotherapy Resistance: A Proteomic Perspective”
by Davide Perico and Pierluigi Mauri
Proteomes 2025, 13(2), 25; https://doi.org/10.3390/proteomes13020025
Available online: https://www.mdpi.com/2227-7382/13/2/25

12. “Proteomics in Allopolyploid Crops: Stress Resilience, Challenges and Prospects”
by Tanushree Halder, Roopali Bhoite, Shahidul Islam, Guijun Yan, Md. Nurealam Siddiqui, Md. Omar Kayess and Kadambot H. M. Siddique
Proteomes 2025, 13(4), 60; https://doi.org/10.3390/proteomes13040060
Available online: https://www.mdpi.com/2227-7382/13/4/60

13. “Marine Bioactive Peptides in the Regulation of Inflammatory Responses: Current Trends and Future Directions”
by D. M. N. M. Gunasekara, H. D. T. U. Wijerathne, Lei Wang, Hyun-Soo Kim and K. K. A. Sanjeewa
Proteomes 2025, 13(4), 53; https://doi.org/10.3390/proteomes13040053
Available online: https://www.mdpi.com/2227-7382/13/4/53

14. “Uncovering Enzyme-Specific Post-Translational Modifications: An Overview of Current Methods”
by Nashira H. Ridgeway and Kyle K. Biggar
Proteomes 2025, 13(3), 37; https://doi.org/10.3390/proteomes13030037
Available online: https://www.mdpi.com/2227-7382/13/3/37

15. “Unraveling the Central Role of Global Regulator PprI in Deinococcus radioduransThrough Label-Free Quantitative Proteomics”
by Siyu Zhu, Feng Liu, Hao Wang and Yongqian Zhang
Proteomes 2025, 13(2), 19; https://doi.org/10.3390/proteomes13020019
Available online: https://www.mdpi.com/2227-7382/13/2/19

16. “Comparative Label-Based Proteomics of Venoms from Echis ocellatus, Naja nigricollis, and Bitis arietans”
by Abdulbaki Alfa-Ibrahim Adio, Samuel Odo Uko, Jiddah Muhammad Lawal, Ibrahim Malami, Nafiu Lawal, Amina Jega Yusuf Jega, Bilyaminu Abubakar, Muhammad Bashir Bello, Kasimu Ghandi Ibrahim, Murtala Bello Abubakar et al.
Proteomes 2025, 13(3), 31; https://doi.org/10.3390/proteomes13030031
Available online: https://www.mdpi.com/2227-7382/13/3/31

17. “Systems Biology of Recombinant 2G12 and 353/11 mAb Production in CHO-K1 Cell Lines at Phosphoproteome Level”
by Eldi Sulaj, Felix L. Sandell, Linda Schwaigerlehner, Gorji Marzban, Juliane C. Dohm and Renate Kunert
Proteomes 2025, 13(1), 9; https://doi.org/10.3390/proteomes13010009
Available online: https://www.mdpi.com/2227-7382/13/1/9

18. “Identifying Endogenous Proteins of Perennial Ryegrass (Lolium perenne) with Ex Vivo Antioxidant Activity”
by Kathrine Danner Aakjær Pedersen, Line Thopholm Andersen, Mads Heiselberg, Camilla Agerskov Brigsted, Freja Lyngs Støvring, Louise Mailund Mikkelsen, Sofie Albrekt Hansen, Christian Enrico Rusbjerg-Weberskov, Mette Lübeck and Simon Gregersen Echers
Proteomes 2025, 13(1), 8; https://doi.org/10.3390/proteomes13010008
Available online: https://www.mdpi.com/2227-7382/13/1/8

19. “Knowledge Discovery in Databases of Proteomics by Systems Modeling in Translational Research on Pancreatic Cancer”
by Mathilde Resell, Elisabeth Pimpisa Graarud, Hanne-Line Rabben, Animesh Sharma, Lars Hagen, Linh Hoang, Nan T. Skogaker, Anne Aarvik, Magnus K. Svensson, Manoj Amrutkar et al.
Proteomes 2025, 13(2), 20; https://doi.org/10.3390/proteomes13020020
Available online: https://www.mdpi.com/2227-7382/13/2/20

20. “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
Proteomes 2025, 13(3), 32; https://doi.org/10.3390/proteomes13030032
Available online: https://www.mdpi.com/2227-7382/13/3/32