In collaboration with the Tamir Lab at UNC Chapel Hill, ProtiFi evaluated the Si-Trap™ as a true multi-omics workflow: one sample in, multiple omics out, without sacrificing analytical quality. Using MCF7 ER+ breast cancer cells, the Si-Trap™ was compared directly with a conventional urea-based proteomics method and a standard metabolite extraction. Si-Trap™ delivered greater proteome depth than urea while maintaining comparable metabolite detection. Across every proteomic comparison, the Si-Trap™ identified more proteins than the urea method. This improvement was observed in global proteome profiling as well as phosphoproteome and tyrosine phosphoproteome analyses, showing that the benefit was not limited to a single protein readout (Figures 1 and 2). Rather than simplifying sample preparation at the expense of sensitivity, the Si-Trap™ increased protein identifications while still supporting metabolomics from the same preparation. Metabolomics results were similarly encouraging. In positive ion mode, the Si-Trap™ matched the standard workflow, with 81 metabolites detected in each case. In negative ion mode, the Si-Trap™ detected 83 metabolites compared with 85 for the standard method. These findings show that Si-Trap™ preserved broad metabolite detection while delivering stronger proteomic depth (Figure 3). The Si-Trap™ thus removes one of the biggest barriers in multi-omics research: the need to choose between simplicity and analytical depth. By generating high-quality metabolomic and proteomic fractions from a single workflow, Si-Trap™ helps researchers gain more insight from every sample.

The Si-Trap™: fast, reproducible single-sample multi-omics!Multi-omics has enormous scientific value: biomolecules don't act in isolation and proteins, metabolites and lipids work together to effect life. Analyzing them together reveals more than studying any single class yet sample prep workflows remain omics-specific: split a sample (or get sequential slices) and independently work up each fraction. That's more handling, more variability and less confidence that the resulting datasets are truly paired: sample preparation and pre-analytical variation tend to be the largest sources of variability. Sample prep has simply lagged behind our multi-omics advances; we needed a better solution! Some approaches tried to address this. Methyl tert-butyl ether (MTBE)-based biphasic extraction (1) can separate a sample into a lipid-rich organic phase, an aqueous metabolite phase, and an insoluble protein-containing residue. SIMPLEX (2) built on this concept using a water/methanol/MTBE extraction, but at the cost of substantial sample manipulation that clogs automation. The Si-Trap™ was designed to solve that problem: one sample, multiple molecular classes, one integrated workflow (3). It gives truly integrated multi-omics sample preparation from a single sample. No splitting, no separate sample prep pipelines and no pellet handling. One protocol generates multiple analysis-ready omics fractions from the same biological input. It is designed for automation and delivers single-digit coefficients of variation. It's especially helpful where you have limited-input samples, biopsies or translational studies: all the situations where sample splitting increases variability and reduces data quality. The workflow begins with strong, detergent-free sample dissolution. After neutralization and denaturation with organic solvent, proteins are captured within derivatized Si-Trap™ pores through weak-affinity interactions. Metabolites and lipids pass through in a mass spectrometry-compatible format. The trapped proteins are then processed and digested in situ with the protease of choice to yield analysis-ready peptides. For a separate lipid fraction, use the optional lipid solution. In ProtiFi’s HuH-7 cell comparison, Si-Trap™ matched or exceeded standard S-Trap™ proteomic depth while producing higher signal for 93% of detected metabolites compared to a conventional acetonitrile extraction. Multi-omics sample preparation should be simple, reproducible, scalable and practical for real-world labs. Since sample preparation is already part of every workflow, why not recover all the major molecular fractions from the same sample? One sample in, multiple molecular classes and integrated biology out! Read more about Si-Trap™ in our previous post here. ReferencesMatyash V, Liebisch G, Kurzchalia TV, Shevchenko A, Schwudke D. Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics. J Lipid Res. 2008;49(5):1137–1146.Coman C, Solari FA, Hentschel A, Sickmann A, Zahedi RP, Ahrends R. Simultaneous Metabolite, Protein, Lipid Extraction (SIMPLEX): A Combinatorial Multimolecular Omics Approach for Systems Biology. Mol Cell Proteomics. 2016;15(4):1453–1466.Zougman A, Wilson JP, Roberts LD, Banks RE. Detergent-Free Simultaneous Sample Preparation Method for Proteomics and Metabolomics. J Proteome Res. 2020;19(7):2838–2844.  

Multi-omics workflows promise deeper biological insight, but sample preparation remains a significant bottleneck. Proteomics and metabolomics are typically collected in separate, parallel workflows, increasing handling and technical variability. Without a unified approach that generates multiple analysis-ready fractions from a single sample, reproducibility and scalability become harder to achieve.   To address this need, we present the Si-Trap™ (Simultaneous Trapping), a high-throughput, detergent-free multi-omics sample preparation platform designed to separate and capture proteins, lipids, and metabolites from one sample with inter- and intra-run reproducibility. The workflow starts with detergent-free lysis, followed by neutralization and organic-solvent denaturation. Proteins are captured within derivatized pores through weak-affinity interactions, while metabolites flow through as a small-molecules fraction compatible with direct mass spectrometry analysis. Trapped proteins are processed in situ on the 96-well plate (denaturation, reduction, and alkylation), digested with the user’s protease of choice, and peptides are subsequently eluted for LC-MS. We also offer an optional lipid extraction solution, that allows for biphasic separation and collection of lipids from the same sample.   Using HuH-7 cells under PFAS exposure as a representative model, we found that Si-Trap™ matched standard S-Trap™ proteomics depth while outperforming a standard ACN:MeOH extraction for 39 of 42 detected metabolites, delivering 1.0- to 7.5-fold higher signal. The Si-Trap™ also detected trends in biologically relevant metabolites that were not observed with the standard workflow. The Si-Trap™ can outperform conventional metabolomics extraction methods, without compromising proteomic recovery and depth.  By eliminating parallel prep workflows, Si-Trap™ reduces handling and variability while supporting scalable, automation-ready processing in a 96-well format. The result is a practical, time-saving, and cost-effective path to reproducible multi-omics sample preparation. Spend less time splitting samples and troubleshooting prep, and more time generating LC-MS data you can trust. Ongoing work is evaluating additional molecular classes to further expand coverage and maximize information recovered from samples.  Be on the lookout- Si-Trap™ is launching this month!