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Tryp-N™: Better, More Certain Monoclonal Antibody Peptide Mapping

A new study highlights how Tryp-N™ is highly effective in LC-MS peptide mapping of monoclonal antibodies. Using NISTmAb, bevacizumab, cetuximab, and trastuzumab, Sargautis and Thiede show how Tryp-N delivers sequence coverage comparable to and greater than trypsin, while also providing distinctly complementary fragmentation. Across all four antibodies, Tryp-N™ generated more peptide-spectrum matches than trypsin, with reported increases of 59% for trastuzumab, 35% for NISTmAb, 8% for cetuximab, and 7% for bevacizumab. For trastuzumab, Tryp-N™ achieved 100% sequence coverage for both heavy and light chains. Combining both enzymes further improved overall sequence coverage. The greatest benefit was increased confidence in site-specific localization of modifications. Trypsin and Tryp-N™ both cleave at K/R, but on opposite sides. This produces complementary fragmentation patterns: tryptic peptides usually have strong y-ion series while Tryp-N™ yields strong b-ions. This orthogonality is particularly useful in determining sites of change like deamidation, oxidation, or single-amino-acid variants (SAVs); often, needed fragmentation ions may be too low in intensity or simply completely absent exactly in the regions needed for unambiguous site localization. The authors demonstrate that Tryp-N™ enabled confident localization and verification of the true site of such modifications, especially where spectra were obscured by noisy fragmentation. The study also emphasized that software alone can misassign modified sites, especially in challenging spectra. Careful manual inspection of MS/MS data and/or use of multiple proteases is essential when high-confidence localization is required, and in particular when one digest gives ambiguous site assignments. In sum, the study found Tryp-N™ as an exceptionally valuable mirror protease to trypsin. As a mirror protease to trypsin, it adds orthogonal evidence exactly where analytical certainty demands it, making Tryp-N™ especially useful for biosimilar comparability, sequence confirmation, multi-attribute method workflows, post-translational modification localization, and low-level variant analysis. Domantas Sargautis, Bernd Thiede Journal of Pharmaceutical and Biomedical Analysis 272 (2026) 117361 DOI: 10.1016/j.jpba.2026.117361 Read more about Tryp-N™ here: About Tryp-N™ – ProtiFi

By |2026-04-10T02:46:33+00:00Apr 10, 2026|Article|0 Comments

How the Si-Trap™ Enables True Multi-Omics: From Proteins, to Lipids, to Metabolites, All in One Workflow

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! 

By |2026-03-10T17:29:16+00:00Mar 10, 2026|Article|0 Comments

What to Expect at US HUPO 2026: New Technologies and Where to Find ProtiFi

Catch ProtiFi at US HUPO 2026 in St. Louis, MO at booth #21! We are excited to join leading scientists, researchers, and industry experts on the cutting edge of science on February 22 – 25th. What should you expect to see from ProtiFi? Check it out below. The highly sought after, first of its kind, multi-omics technology, the Si-Trap™. Be the first to see this industry leading technology set to launch in March. The Si-Trap™ is perfect for those with precious samples and looking for a cost-effective solution; allowing preparation of lipids, metabolites, and proteins all in one workflow! Find more information here or visit our poster during Poster Session 1 at poster P16.25. Do you have a need for more rapid sample preparation? Come by and check out the S-Trap™ Turbo™ Mini Plate and Kit. Stronger binding with less capture matrix allows smaller elution volumes elimination the need for additional concentration steps (and time). Designed for high-throughput workflows, the S-Trap™ Turbo™ integrates seamlessly into 96-well processing and automation platforms, making it well-suited for large cohort studies, discovery proteomics, and comparative screening applications. Need help with data analysis? SimpliFi™ makes organizing and visualizing complex omics data simple. Stop by our poster during Poster Session 2 at poster P04.14. Stop by the ProtiFi booth and we would be happy to discuss any of these new exciting products with you as well as the newly released S-Trap™ Micro Plate and other S-Trap™ products!

By |2026-02-27T02:08:21+00:00Feb 20, 2026|Article|0 Comments
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