Researchers at Cold Spring Harbor Laboratory have developed a new mass spectrometry method, enhancing instrument performance to provide more sensitive scans. This advancement could improve drug target identification and assist scientists in addressing persistent questions about human health and biology. The study was published in Analytical Chemistry.
Mass spectrometry, seen here, measures molecular weight by injecting ions through a chamber and timing how long it takes each one to reach a sensor. Imagine throwing a tennis ball and a medicine ball at a wall. You can determine their weight based on how fast they accelerate and how long it takes them to reach the wall. Image Credit: Cold Spring Harbor Laboratory.
Weight is significant. In the kitchen, it can indicate using too little or too much of an ingredient. For scientists, a molecule's weight can help define its composition. This can show if a potential drug is affecting the body or is ineffective. Weight can also reveal the composition of tumors, possibly impacting treatment choices. For these and other measurements, researchers use a technique called mass spectrometry.
A mass spectrometer is essentially a very precise scale. Imagine a bucket full of different molecules. Using mass spectrometry, you can figure out what molecules and how many are in that bucket. This enables researchers to try to answer questions like, ‘Are there different proteins, lipids, or other small molecules in one tumor versus another?’
Paolo Cifani, Research Associate Professor, Cold Spring Harbor Laboratory (CSHL)
Cifani and his team at CSHL’s Mass Spectrometry facility have created a new technique to enhance the performance of their instruments. Their innovation could improve drug target discovery, assisting scientists in answering long-standing questions about human health and biology.
In identifying molecules within complex mixtures, mass spectrometer sensitivity was believed to be primarily dictated by speed. Standard scans involve transitioning molecules to a gaseous state. Their ions are then measured sequentially by taking "snapshots" inside the "bucket" every few seconds. However, if too many ions accumulate, they can begin interacting, which disrupts the scan. So, “it seems intuitive that the faster you go, the more you can sequence,” Cifani notes.
Speed is always a factor. But potentially interesting molecules can be overlooked because they’re not seen in the snapshot, as the spectrometer gets ‘blinded’ by more abundant ions. Our new technique looks to remedy that.
Paolo Cifani, Research Associate Professor, Cold Spring Harbor Laboratory (CSHL)
Cifani compares it to a sorting system. Instead of measuring everything in the chamber simultaneously, the Cifani lab divides scans into "bins." If a molecule is present at significantly higher levels, it fills only one bin, not the others.
Our method is much better at measuring differences in concentration. That’s very important when studying a drug versus a placebo.
Paolo Cifani, Research Associate Professor, Cold Spring Harbor Laboratory (CSHL)
The lab is currently working to improve and broaden access to its new technique. Numerous CSHL core facilities provide technical expertise to researchers at the Laboratory and to other institutions. Cifani and his team believe their technique will be beneficial to the scientific community.
“This is a proof of concept. We’re ready to inspire discovery, worldwide,” Paolo Cifani says.
The research was funded by the CSHL/Northwell Health Affiliation and the Simons Foundation.
Journal Reference:
Panepinto, M. C., et al. (2025). High Dynamic Range Peptide Mass Spectrometry Using Segmented Precursor Ion Accumulation. Analytical Chemistry. DOI: 10.1021/acs.analchem.5c04349. https://pubs.acs.org/doi/10.1021/acs.analchem.5c04349.