New Proteomics Software Enables High-Flow Data Analysis
The research-stage engine identifies thousands of proteins at flow rates previously incompatible with standard search tools.
Updated on Oct. 22, 2026 in Biotech
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Researchers have released msallsearchpy, a new proteomics search engine capable of identifying and quantifying proteins at flow rates as high as 400 µL/min. The research-stage software supports data-independent acquisition (DIA), data-dependent acquisition (DDA), and MS1-only acquisition methods.
Why it matters
High-flow proteomics offers a more efficient workflow than standard nano-liquid chromatography. By enabling data analysis at increased flow rates, this tool addresses throughput limitations currently hindering large-scale proteome research.
In a controlled test, msallsearchpy successfully identified 2000 proteins from a 20 ng sample at 50 µL/min. Established search engines failed to identify any proteins under these same high-flow conditions.
The players
msallsearchpy
A research-stage proteomics search engine designed to process high-flow mass spectrometry data.
The details
The software processes data acquired via Orbitrap FTMS—a mass spectrometry technique that uses high-frequency electrostatic fields to trap ions—at flow rates up to 400 µL/min. It employs specialized algorithms to parse data from DIA, where all ions are fragmented simultaneously; DDA, which selects specific ions for fragmentation; and MS1-only, which measures intact molecular ions. These methods allow the engine to maintain analytical accuracy as sample speeds increase.
Timeline
October 22, 2026: Official release of the msallsearchpy proteomics software.
The Tech Race
The development represents a shift away from the throughput constraints of traditional nanoLC-based proteome analysis. It aims to accelerate the field by allowing proteomics workflows to move from slower, specialized flow rates to faster, more robust speeds.
Laboratory researchers can now utilize this tool to analyze proteomic samples at significantly higher throughput than current nano-flow standards permit. The software is currently in the research stage and requires access to Orbitrap mass spectrometry data to implement.
The takeaway
This software demonstrates that high-flow proteomics is viable, effectively outperforming established tools at high sample speeds. Researchers should track future benchmarking updates to see how the engine handles real-world, complex biological samples compared to synthetic test sets.
Further reading
For more on emerging analytical techniques, visit Biotech.
More information
Read the complete scientific study paper on the pre-print server.
Source note: This article includes information reported by Biorxiv.
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