Proteomics最新文献

The field of clinical proteomics has seen enormous growth in the past 20 years, with over 40,000 scientific manuscripts published to date. At the same time, actual clinical application of the reported findings is obviously scarce. In this viewpoint article, we discuss the key issues that may be responsible for this apparent lack of success. We conclude that success must not be assessed based on the number of publications, but via the impact on patient management and treatment. We proceed with specific suggestions for potential solutions, which include keeping a strict focus on potential patient benefit. We hope this article can help shape the field, so it can in fact deliver on its realistic promise to bring significant improvement in management and care to patients.

Fluctuating salinity is symptomatic of climate change challenging aquatic species. The melting of polar ice, rising sea levels, coastal surface and groundwater salinization, and increased evaporation in arid habitats alter salinity worldwide. Moreover, the frequency and intensity of extreme weather events such as rainstorms and floods increase, causing rapid shifts in brackish and coastal habitat salinity. Such salinity alterations disrupt homeostasis and ultimately diminish the fitness, of aquatic organisms by interfering with metabolism, reproduction, immunity, and other critical aspects of physiology. Proteins are central to these physiological mechanisms. They represent the molecular building blocks of phenotypes that govern organismal responses to environmental challenges. Environmental cues regulate proteins in a concerted fashion, necessitating holistic analyses of proteomes for comprehending salinity stress responses. Proteomics approaches reveal molecular causes of population declines and enable holistic bioindication geared toward timely interventions to prevent local extinctions. Proteomics analyses of salinity effects on aquatic organisms have been performed since the mid-1990s, propelled by the invention of two-dimensional protein gels, soft ionization techniques for mass spectrometry (MS), and nano-liquid chromatography in the 1970s and 1980s. This review summarizes the current knowledge on salinity regulation of proteomes from aquatic organisms, including key methodological advances over the past decades.

Mass spectrometry is a critical tool to understand complex changes in biological processes. Despite significant advances in search engine technology, many spectra remain unassigned. This research evaluates the performance of three rescoring platforms, Oktoberfest, MS²Rescore, and inSPIRE, using MaxQuant output. The results indicated a substantial increase in identifications at the peptide level (40%-53%) and PSM level (64%-67%). However, some peptides were lost due to limitations in processing posttranslational modifications (PTMs)-with up to 75% of lost peptides exhibiting PTMs. Each platform displayed distinct strengths and weaknesses. For instance, inSPIRE performed best in terms of peptide identifications and unique peptides, while MS²Rescore performed better for PSMs at higher FDR values. Differences in platform performance stemmed from different sources: original search engine feature selection, type of ion series predicted, retention time predictor, and PTMs compatibility. Overall, inSPIRE showed a superior ability to harness original search engine results. Taken all together, rescoring platforms clearly outperformed original search results; however, they demanded additional computation time (up to 77%) and manual adjustments. The findings here underline the necessity of integrating rescoring platforms into current proteomics pipelines but also address some challenges in their implementation and optimization. Future integrated platforms may help enhance adoption.

Metaproteomics enables the large-scale characterization of microbial community proteins, offering crucial insights into their taxonomic composition, functional activities, and interactions within their environments. By directly analyzing proteins, metaproteomics offers insights into community phenotypes and the roles individual members play in diverse ecosystems. Although database-dependent search engines are commonly used for peptide identification, they rely on pre-existing protein databases, which can be limiting for complex, poorly characterized microbiomes. De novo sequencing presents a promising alternative, which derives peptide sequences directly from mass spectra without requiring a database. Over time, this approach has evolved from manual annotation to advanced graph-based, tag-based, and deep learning-based methods, significantly improving the accuracy of peptide identification. This Viewpoint explores the evolution, advantages, limitations, and future opportunities of de novo sequencing in metaproteomics. We highlight recent technological advancements that have improved its potential for detecting unsequenced species and for providing deeper functional insights into microbial communities.