How next-generation proteomics is decoding the language of life

By Hugo Francisco de SouzaReviewed by Susha Cheriyedath, M.Sc.Apr 13 2026

From single-molecule fluorescence to nanopore readouts, emerging platforms are opening a new window into the hidden diversity of proteins that mass spectrometry can miss.

Review: The Next Generation of Protein Sequencing and Analysis Methods. Image Credit: Corona Borealis Studio / Shutterstock

In a recent review published in the Annual Review of Analytical Chemistry, researchers at the University of Washington, Seattle, synthesized 137 scientific papers to elucidate the current status and future potential of proteomics. The review highlights that technological advances are beginning to reshape the field, pushing it from bulk measurements toward the high-resolution analysis of individual molecules.

While mass spectrometry (MS) remains the current gold standard, recent studies indicate that it struggles to capture the full diversity of "proteoforms" (various protein versions that can arise from a single gene).

The review reveals how emergent proteomic methods, some of which have reached or are nearing commercial implementation, have the potential to transform future biological discovery by providing a deeper, more sensitive look at the molecular machinery of life.

Proteomics Background and Mass Spectrometry Limits

Since the discovery of deoxyribonucleic acid (DNA) (Friedrich Miescher, 1869) and its subsequent structural elucidation (Watson & Crick, 1953), biological research has, for decades, focused on analyzing the genome to unravel the mysteries of life. However, more recent studies argue that this genomic focus largely stems from the relative ease of DNA amplification and sequencing, which fail to fully capture phenotypic functionality.

In contrast, the proteome (a holistic snapshot of protein expression) is a more direct indicator of biological function. However, unlike their DNA counterparts, proteins cannot be easily amplified, making their analysis significantly harder. Furthermore, while DNA is composed of only four building blocks, proteins are made of 20 chemically diverse amino acids, thereby posing substantial computational limitations for their analysis.

Research over the past two decades has established that a single gene can produce countless biologically relevant proteoforms through processes such as proteolysis, alternative splicing, and posttranslational modifications (PTMs; chemical changes to a protein after it is made). Understanding these variations is now known to be important for understanding disease biology and for informing biomedical research in areas such as Alzheimer’s disease and cancer.

Unfortunately, traditional tools such as mass spectrometry (MS; a technique that identifies molecules based on their mass-to-charge ratio) often miss low-abundance species or fail to provide full sequence coverage, thereby hampering research progress. The review highlights these limitations and underscores the urgent need for "next-generation" protein sequencing that operates at the single-molecule level.

Next-Generation Proteomics Review Scope

This review synthesizes the current landscape of protein analysis by focusing on next-generation proteomic platforms that have recently reached or are nearing commercialization. It collates outcomes from 137 peer-reviewed publications and centers on two major technology groups, while also acknowledging other emerging approaches:

Fluorescence-based methods: These techniques leverage light-emitting tags to enhance the identification of amino acids. They include technologies such as "fluorosequencing" (Erisyon), in which specific residues are labeled and then sequentially removed via Edman degradation, and Quantum-Si’s implementation of a semiconductor chip to monitor the binding kinetics of "recognizer" molecules to the protein's end. The review also discusses Nautilus Biotechnology’s digital proteomics mapping platform, which uses iterative binding patterns to quantify proteoforms at the single-molecule level.

Nanopore methods: This approach involves threading a linearized protein through a nanometer-sized hole. As the protein passes through, it disrupts an electric current in a manner specific to its sequence. This is predominantly achieved by using inorganic "solid-state" pores or biological "pore proteins" embedded in a membrane. Some methods further incorporate molecular motors (e.g., unfoldase ClpX) to pull the protein through at a controlled speed.

Fluorescence and Nanopore Proteomics Advances

The review highlights significant milestones achieved by conventional and emergent proteomic technologies. For example, Quantum-Si’s "Platinum" system (released in 2022) was the first commercial entry into this space. Since its inception, their technology has expanded to recognize approximately 14 amino acids (as of late 2025), enabling coverage of ~83.5% of the human proteome.

Erisyon’s advances in protein fingerprinting technologies have shown that labeling just four amino acids (lysine, aspartate/glutamate, tyrosine, and tryptophan) should, according to modeling studies, be sufficient to uniquely identify ~95% of proteins in the human proteome. Notably, Erisyon’s platform has already demonstrated the ability to identify proteins from zeptomole-scale mixtures in proof-of-concept experiments.

Nautilus Biotechnology’s IMaP (iterative mapping of proteoforms) assay has identified 130 distinct tau (a neurodegenerative disease-linked protein) proteoform groups, revealing complex phosphorylation patterns that would be difficult to capture in bulk samples.

Simultaneously, recent advances in nanopore (“rereading”) technologies have significantly improved accuracy within specific experimental systems, with a study (using a protein-processive motor) revealing that while a single pass might only classify amino acids correctly 28% of the time, 10 "rereads" of the same molecule improved accuracy to 61%. Furthermore, functionalized pores leveraging Ni2+ ions have been shown to achieve the sensitivity required to distinguish all 20 proteinogenic amino acids.

Future Role of Single-Molecule Proteomics

This review concludes that while emergent single-molecule proteomics approaches are nearing commercial maturity, they remain complementary to traditional MS-based approaches.

While the application of specialized protein-movement-facilitating “tags” in large-scale proteomics remains a major practical hurdle, these technologies are poised to become a staple of biological research, offering a high-definition view of the molecular variations that drive human health and disease.