I recommend here examples of the best papers in the Proteomics field for the new students and scholars to read and refer to.
These papers are classified into Leading Reviews, Methods, Softwares, and Applications in Biology/ Clinical questions, with their PubMed ID listed.
27629641: A recent review by Aebersold and Mann on Proteomics.
12634793: The first review by Aebersold and Mann, cited >6500 times.
27104977: mRNA-protein correlation-why proteomics?
20622845: How to select a quantitative proteomic strategy when needed.
18854821: Everything about S/MRM.
22261725: SWATH-MS, why & how?
28065596: Where is TMT now (by Gygi's group).
22984071: A classic cross linking study.
17327847: Target-decoy, how False discovery is controlled in Proteomics?
19029910: MaxQuant, a widely used data toolkit in shotgun.
20147306: Proteomic data: now you see it!
14632076: A statistical model for identifying proteins.
18806791: Spectral library, the essential concept for DIA proteomics.
16615898: Classic, organ and organelle protein expression in mouse.
17081983: Global, in vivo, and site-specific phosphorylation dynamics.
22068332: The quantitative proteome of a human cell line.
28514442: Bioplex, the protein-protein interaction architecture.
28495876: Large-scale antibody based proteomics.
24132637: A blood-based proteomic classifier for lung cancer.
24870543: A important draft of the human proteome.