Proteomes MDPI

Take a look at the Proteomes 2025 Annual Report to learn about the journal's growth, achievements, and key developments over the past year

https://brnw.ch/21x33xG

Proteomes Annual Report Card 2025 We begin by expressing our sincere thanks to all Editorial Board Members, Guest Editors, Reviewers, Authors, and the staff in the Editorial Office for their dedicated service in support of Proteomes [...]

We are pleased to share this article published in Proteomes: Enhanced Electrophoretic Depletion of Sodium Dodecyl Sulfate with Methanol for Membrane Proteome Analysis by Mass Spectrometry

https://brnw.ch/21x2VQh

Enhanced Electrophoretic Depletion of Sodium Dodecyl Sulfate with Methanol for Membrane Proteome Analysis by Mass Spectrometry Membrane proteins are underrepresented during proteome characterizations, primarily owing to their lower solubility. Sodium dodecyl sulfate (SDS) is favored to enhance protein solubility but interferes with downstream analysis by mass spectrometry. Here, we present an improved workflow for SDS deple...

This article is now available in Proteomes: Enabling Next-Generation Mass Spectrometry-Based Proteomics: Standards, Proteoform Resolution, and FAIR, Reproducible, and Quantitative Analysis

https://brnw.ch/21x2TFo

Enabling Next-Generation Mass Spectrometry-Based Proteomics: Standards, Proteoform Resolution, and FAIR, Reproducible, and Quantitative Analysis Recent advances in mass spectrometry, data-independent acquisition, proteoform-resolving workflows, and multi-omics integration have significantly expanded the scale and scope of proteomics. However, the reuse and translational application of these datasets are limited by inconsistent standards, ins...

This article is now available in Proteomes: Prospective ICH Q2(R2)-Aligned Total-Error Validation of Label-Free Untargeted Proteomics for Host Cell Protein Quantification in Biotherapeutics

https://brnw.ch/21x2PtN

Prospective ICH Q2(R2)-Aligned Total-Error Validation of Label-Free Untargeted Proteomics for Host Cell Protein Quantification in Biotherapeutics Background: Untargeted proteomics enables quantitative host cell protein (HCP) determination in biotherapeutics, yet no workflow has been validated under ICH Q2(R2) for regulated quality control. Methods: A prospective total-error (TE) validation of label-free ddaPASEF proteomics was performed. A st...

We are pleased to share this article published in Proteomes: How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction?

https://brnw.ch/21x2J9x

How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction? This perspective article is concerned with the question of how proteomics, which is a core technique of systems biology that is deeply embedded in the multi-omics field of modern bioresearch, can help us better understand the molecular pathogenesis of complex diseases. As an illustrative example of....

This article is now available in Proteomes: Proteostasis, Assisted Reproductive Technologies, and Neurodevelopmental Differences: An Integrative Perspective

https://brnw.ch/21x2GQY

Proteostasis, Assisted Reproductive Technologies, and Neurodevelopmental Differences: An Integrative Perspective Proteostasis, defined as the coordinated regulation of protein synthesis, folding, trafficking, and degradation, is essential for maintaining cellular integrity and supporting normal development. During reproduction and early life stages, efficient proteostasis is crucial for gamete quality, success...

Proteomes has announced the Top 20 Viewed Papers in 2025. You are welcome to take a look!
https://brnw.ch/21x2C7C

We are pleased to share this article published in Proteomes: Observations from the Proteomics Bench

https://brnw.ch/21x2w79

Observations from the Proteomics Bench Many challenges in proteomics result from the high-throughput nature of the experiments. This paper first presents pre-analytical problems, which still occur, although the call for standardization in omics has been ongoing for many years. This article also discusses aspects that affect bioinformatic...

This article is now available in Proteomes: Beyond Reanalysis: Critical Issues in Data Reuse for Solid Tumor Proteomics
https://brnw.ch/21x2nvi

Computational Phosphosite-Specific Network Analysis of YES1 Y426 Reveals Cancer-Associated Phosphorylation Patterns Background: YES1 is an Src family non-receptor tyrosine-protein kinase that regulates cell growth, migration, survival, and oncogenic signaling. Although YES1 activation mechanisms and substrates have been extensively studied, its phosphosite-specific regulation across diverse biological contexts re...

This article is now available in Proteomes: Beyond Reanalysis: Critical Issues in Data Reuse for Solid Tumor Proteomics

https://brnw.ch/21x2ixQ

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