Mass Spectrometry-Based Proteomic Analysis

Mass spectrometry–based proteomics encompasses a suite of analytical approaches designed to identify, characterise and quantify the full complement of proteins in biological samples. Central to these methods is the conversion of complex protein mixtures into peptide fragments, their ionisation and separation according to mass-to-charge ratio, and the acquisition of tandem mass spectra for sequence assignment. Modern workflows integrate both data-dependent acquisition, in which the most abundant ions are selected for fragmentation, and data-independent acquisition, where predefined m/z windows are systematically interrogated. Advances in high-resolution instrumentation, labelling strategies and computational algorithms have driven leaps in sensitivity, throughput and reproducibility. As a result, proteomics underpins diverse fields from basic cell biology and systems medicine to biomarker discovery and precision therapeutics. Emerging single-cell and spatial proteomic techniques now resolve cellular heterogeneity and tissue architecture, while phosphoproteomic and other post-translational-modification analyses elucidate dynamic signalling networks. Together, these developments have established mass spectrometry as a cornerstone of modern molecular science, enabling global surveys of protein expression, modification and interaction across health and disease contexts.

Research from Nature Portfolio

Ultra-fast narrow-window data-independent acquisition has redefined throughput and depth by coupling high-resolution precursor scans with >200 Hz MS/MS fragmentation. This approach profiles hundreds of proteomes per day with unprecedented coverage, quantifying over 10,000 human protein groups in under thirty minutes and delivering robust performance in mixed-species benchmarks. A complementary study has mapped the intrinsic substrate specificity of more than 300 human serine/threonine kinases using synthetic peptide libraries, creating a kinome-wide atlas that links phosphorylation sites to their catalytic enzymes and reveals unexpected network compensation under perturbation. In parallel, spatial single-cell proteomics has been extended to intact tissues through an integrated pipeline of high-content imaging, laser microdissection and multiplexed mass spectrometry. This technique resolves location-dependent proteome zonation in murine liver down to individual hepatocytes, with machine-learning models predicting spatial patterns directly from images, thereby bridging molecular profiling and histological context.

Mass Spectrometry-Based Proteomic Analysis publication trend

The graph below shows the total number of articles in mass spectrometry-based proteomic analysis across all publications each year (not limited to Nature Index journals).

Technical terms

Mass spectrometry: Analytical method that measures mass-to-charge ratios of ionised peptides to identify and quantify proteins.

Data-independent acquisition (DIA): MS strategy that fragments all ions within sequential mass windows to enable comprehensive and reproducible peptide detection.

Data-dependent acquisition (DDA): Mode in which the most intense precursor ions are selected in real time for fragmentation and identification.

Label-free quantification: Approach that derives relative protein abundance from peptide signal intensities without stable isotope labelling.

Phosphoproteomics: Study of protein phosphorylation events by enriching phosphopeptides for targeted mass spectrometric analysis.

Single-cell proteomics: Techniques that measure the proteome of individual cells to reveal cellular heterogeneity.

Spatial proteomics: Mapping of protein distributions within tissues or cellular compartments, often combining imaging with mass spectrometry.

References

1. Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition. Nature Biotechnology (2024).
2. An atlas of substrate specificities for the human serine/threonine kinome. Nature (2023).
3. Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome. Nature Methods (2023).
4. Proteogenomic data and resources for pan-cancer analysis. Cancer Cell (2023).
5. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Research (2021).