A Rapid One-Pot Workflow for Sensitive Microscale Phosphoproteomics.

Compared to advancements in single-cell proteomics, phosphoproteomics sensitivity has lagged behind due to low abundance, complex sample preparation, and substantial sample input requirements. We present a simple and rapid one-pot phosphoproteomics workflow (SOP-Phos) integrated with data-independent acquisition mass spectrometry (DIA-MS) for microscale phosphoproteomic analysis. SOP-Phos adapts sodium deoxycholate based one-step lysis, reduction/alkylation, direct trypsinization, and phosphopeptide enrichment by TiO2 beads in a single-tube format. By reducing surface adsorptive losses via utilizing n-dodecyl ß-d-maltoside precoated tubes and shortening the digestion time, SOP-Phos is completed within 3-4 h with a 1.4-fold higher identification coverage. SOP-Phos coupled with DIA demonstrated >90% specificity, enhanced sensitivity, lower missing values (<1%), and improved reproducibility (8%-10% CV). With a sample size-comparable spectral library, SOP-Phos-DIA identified 33,787 ± 670 to 22,070 ± 861 phosphopeptides from 5 to 0.5 µg cell lysate and 30,433 ± 284 to 6,548 ± 21 phosphopeptides from 50,000 to 2,500 cells. Such sensitivity enabled mapping key lung cancer signaling sites, such as EGFR autophosphorylation sites Y1197/Y1172 and drug targets. The feasibility of SOP-Phos-DIA was demonstrated on EGFR-TKI sensitive and resistant cells, revealing the interplay of multipathway Hippo-EGFR-ERBB signaling cascades underlying the mechanistic insight into EGFR-TKI resistance. Overall, SOP-Phos-DIA is an efficient and robust protocol that can be easily adapted in the community for microscale phosphoproteomic analysis.

Recent advances in microfluidics for single-cell functional proteomics.

Single-cell proteomics (SCP) reveals phenotypic heterogeneity by profiling individual cells, their biological states and functional outcomes upon signaling activation that can hardly be probed via other omics characterizations. This has become appealing to researchers as it enables an overall more holistic view of biological details underlying cellular processes, disease onset and progression, as well as facilitates unique biomarker identification from individual cells. Microfluidic-based strategies have become methods of choice for single-cell analysis because they allow facile assay integrations, such as cell sorting, manipulation, and content analysis. Notably, they have been serving as an enabling technology to improve the sensitivity, robustness, and reproducibility of recently developed SCP methods. Critical roles of microfluidics technologies are expected to further expand rapidly in advancing the next phase of SCP analysis to reveal more biological and clinical insights. In this review, we will capture the excitement of the recent achievements of microfluidics methods for both targeted and global SCP, including efforts to enhance the proteomic coverage, minimize sample loss, and increase multiplexity and throughput. Furthermore, we will discuss the advantages, challenges, applications, and future prospects of SCP.

Analyses of active antioxidant polysaccharides from four edible mushrooms.

Four water-soluble polysaccharides were extracted from Pleurotus eryngii, Flammulina velutipes, Pleurotus ostreatus and white Hypsizygus marmoreus. Using anion exchange and gel permeation chromatography, a neutral and an acidic fraction were purified from each water-soluble polysaccharide. Their molecular weights were all around 20 kDa except that the acidic polysaccharide from Pleurotus ostreatus (named WPOPA) had a lower molecular weight of 5 kDa. Four neutral polysaccharides were mainly composed of galactose (42.7%-69.1%), followed by Man (19.4%-39.3%) and Glc (1.1%-15.9%). Four acidic polysaccharides contained glucose (59.0%-81.8%) as major sugar and minor glucuronic acid (4.5%-9.5%). Acidic polysaccharides exhibited stronger antioxidant activities than neutral fractions, and WPOPA showed the best antioxidant effects. Structural analysis indicated WPOPA had ß-(1 → 6)-glucan backbone branched at O-3 by ß-1,3-d-Glcp, t-ß-d-Glcp and t-ß-d-GlcpA. This investigation would be useful for screening natural antioxidants and significant in developing mushroom polysaccharides as functional foods.