In-source fragmentation (ISF) has emerged as one of the most actively discussed topics in metabolomics. What was once treated as a technical detail is now recognized as a variable that can meaningfully influence feature detection, metabolite annotation, and biological interpretation.
Across peer-reviewed journals and publications, scientists are revisiting fundamental questions:
- To what extent does ISF contribute to the so-called “dark metabolome”?
- How do ion source design and operating conditions shape observed molecular features?
- When does fragmentation obscure biological insight and when is it simply part of the analytical landscape?
Rather than converging on a single conclusion, the metabolomics community is engaging in an open, rigorous conversation.
A Field-Wide Conversation, Not a Consensus
The debate started with several peer-reviewed publications, including:
Recent articles in The Analytical Scientist have further captured the diversity of perspectives shaping the current discussion around ISF and the dark metabolome. In “Lighting the Way Forward for Metabolomics” (December 2025), contributors explore how analytical artifacts, biological complexity, and experimental context intersect in modern metabolomics workflows.
This article is part of a broader series that includes:
- Pieter Dorrestein & Yasin El Abiead, The Dark Metabolome: No Mere Figment?
- Martin Giera & Gary Siuzdak, The Dark Metabolome Debate Continues
- Shuzhao Li, A Call for Context
- Gary Patti, Metabolomics Is Not in Crisis
- Jan-Christoph Wolf, Does In-Source Fragmentation Require a Soft Touch?
- Oliver Jones, The Past, Present, and Future of the “Dark Metabolome”
These perspectives underscore a shared theme: in-source fragmentation cannot be evaluated in isolation. Its significance depends on experimental design, instrumentation, ionization conditions, and the biological questions being asked.
The absence of consensus on the degree of ISF and its contribution to the dark metabolome is not a failure of the field; it is evidence of a community actively refining its tools. methods, and interpretations.
Newomics Does Not Take Sides
We at Newomics do not take sides in this debate.
Scientific progress depends on evidence, reproducibility, and context, not on prescribing interpretations. Rather than declaring ISF inherently good or bad, we focus on enabling researchers to observe, control, and evaluate fragmentation behavior within their own workflows.
Our role is not to settle the debate, but to help scientists generate clearer data so they can draw their own conclusions.
Experimental Capabilities Enabled by Newomics UniESI Platform
Several independent, peer-reviewed studies have demonstrated that the UniESI platform with M3 emitters and MEA chips, “dramatically reduces in-source fragmentation while significantly increasing sensitivity in both positive and negative ESI-MS modes.”
- Investigating the Metabolic Heterogeneity of Cancer Cells Using Functional Single-Cell Selection and nLC Combined with Multinozzle Emitter Mass Spectrometry
- Multinozzle Emitter for Improved Negative Mode Analysis of Reduced Native N‑Glycans by Microflow Porous Graphitized Carbon Liquid Chromatography Mass Spectrometry
- Microflow Liquid Chromatography Coupled to Multinozzle Electrospray Ionization for Improved Lipidomics Coverage of 3D Clear Cell Renal Cell Carcinoma
- Region-specific quantitation of glycosphingolipids in the elderly human brain with Nanoflow MEA Chip Q/ToF mass spectrometry
Collectively, these studies suggest that UniESI can serve as a practical experimental tool for researchers who wish to:
- Minimize unintended fragmentation during ionization
- Preserve intact molecular ions
- Compare datasets generated under different ionization regimes
- Examine how ISF influences feature detection, annotation confidence, and downstream interpretation
Importantly, reduced ISF does not prescribe a biological conclusion. Instead, it provides an alternative ionization environment by enabling controlled comparisons and hypothesis-driven evaluation of ISF’s role.
MS Vendor-Agnostic Evaluation
ISF behavior varies across instrument architectures and source geometries. UniESI was therefore designed as a vendor-agnostic platform, compatible with mass spectrometers from Thermo Fisher Scientific, Bruker, Agilent, Waters, and Shimadzu.
We’re encouraging researchers to check out our metabolomics page for more details and evaluate UniESI directly within their own experimental context using their samples, workflows, and analytical objectives.
This empirical approach mirrors the ethos of the current ISF discussion: test assumptions, generate data, and let evidence guide interpretation.
As the metabolomics community continues to explore the role of in-source fragmentation, Newomics welcomes scientists to experience UniESI firsthand across MS from all five supported vendors.
Test it. Compare it. Challenge it.
The most meaningful insights will come not from taking sides, but from generating better data.
Here is to the Year of Metabolomics!
