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  • Primer
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Peptidomics

Nature Reviews Methods Primers volume 3, Article number: 25 (2023) Cite this article

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Abstract

Peptides are biopolymers, typically consisting of 2–50 amino acids. They are biologically produced by the cellular ribosomal machinery or by non-ribosomal enzymes and, sometimes, other dedicated ligases. Peptides are arranged as linear chains or cycles, and include post-translational modifications, unusual amino acids and stabilizing motifs. Their structure and molecular size render them a unique chemical space, between small molecules and larger proteins. Peptides have important physiological functions as intrinsic signalling molecules, such as neuropeptides and peptide hormones, for cellular or interspecies communication, as toxins to catch prey or as defence molecules to fend off enemies and microorganisms. Clinically, they are gaining popularity as biomarkers or innovative therapeutics; to date there are more than 60 peptide drugs approved and more than 150 in clinical development. The emerging field of peptidomics comprises the comprehensive qualitative and quantitative analysis of the suite of peptides in a biological sample (endogenously produced, or exogenously administered as drugs). Peptidomics employs techniques of genomics, modern proteomics, state-of-the-art analytical chemistry and innovative computational biology, with a specialized set of tools. The complex biological matrices and often low abundance of analytes typically examined in peptidomics experiments require optimized sample preparation and isolation, including in silico analysis. This Primer covers the combination of techniques and workflows needed for peptide discovery and characterization and provides an overview of various biological and clinical applications of peptidomics.

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Fig. 1: Peptides, from analysis to application.
Fig. 2: In silico peptide mining.
Fig. 3: Overview of common peptidomics workflows.
Fig. 4: Quantitation methods for peptidomics.
Fig. 5: From nature to medicine.

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Acknowledgements

Work in the laboratory of C.W.G. has been supported by the Austrian Science Fund (FWF) through projects P32109 and ZK 81B. The work of A.S. and R.D.S. was funded by the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation) under Germany’s Excellence Strategy — EXC 2008-390540038 (UniSysCat) and RTG 2473 ‘Bioactive Peptides’. The work of L.L. is supported by the National Science Foundation (NSF) (CHE-2108223) and National Institutes of Health (NIH) through grants (R01DK071801, R01 AG078794 and RF1AG052324). The work of J.V.S. is supported by the National Institute on Drug Abuse under Award No. P30DA018310 and the National Institute of Neurological Disorders and Stroke (NINDS) through R01NS031609.

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  1. These authors contributed equally: Roland Hellinger, Arnar Sigurdsson, Wenxin Wu, Elena V. Romanova.

Authors and Affiliations

  1. Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria

    Roland Hellinger & Christian W. Gruber

  2. Institut für Chemie, Technische Universität Berlin, Berlin, Germany

    Arnar Sigurdsson & Roderich D. Süssmuth

  3. School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA

    Wenxin Wu & Lingjun Li

  4. Department of Chemistry, University of Illinois, Urbana, IL, USA

    Elena V. Romanova & Jonathan V. Sweedler

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Related links

antiSMASH: https://antismash.secondarymetabolites.org

DeepBGC: https://github.com/Merck/deepbgc

DeepRiPP: http://deepripp.magarveylab.ca

DEREPLICATOR+: https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp

Dictionary of Natural Products: https://dnp.chemnetbase.com/faces/chemical/ChemicalSearch.xhtml

High Definition Imaging: https://www.waters.com/waters/en_US/High-Definition-Imaging-(HDI)-Software/nav.htm?cid=134833914&locale=en_US

ImageQuest: https://www.thermofisher.com/order/catalog/product/10137985

MS-FINDER: http://prime.psc.riken.jp/compms/msfinder/main.html

MSiReader: https://msireader.com/

msiQuant: https://ms-imaging.org/paquan/

NCBI: https://www.ncbi.nlm.nih.gov

SANDPUMA: https://bitbucket.org/chevrm/sandpuma/src/master/

SCiLS Lab: https://www.bruker.com/en/products-and-solutions/mass-spectrometry/ms-software/scils-lab.html

UniProt: https://www.uniprot.org

Supplementary information

Glossary

Fourier transform ion cyclotron resonance mass spectrometers

(FTICR-MS). High-resolution mass analysers that trap ions in a cyclotron radius by applying a fixed magnetic field and an oscillating electronic field. As the ions rotate, an interferogram signal is recorded by electrodes and the useful mass spectrum is extracted with a Fourier transformation.

Hyphenated front-end separation platforms

Platforms that separate the analytes online before they enter the mass spectrometers. Techniques include, but are not limited to, liquid chromatography, gas chromatography, ion mobility spectrometry (IMS), solid-phase extraction (SPE) and capillary electrophoresis.

Ion mobility spectrometry

(IMS). An analytical technique that sorts and separates gas-phase ions based on their mobility in a carrier buffer gas under the influence of an electrical field, which is related to the conformation and 3D shapes of the molecules.

Multiple reaction monitoring

A type of analysis for tandem mass spectrometers providing capabilities for quantitation of analytes. Pre-defined precursor ions (m/z) are selected by the first mass analyser and submitted to a fragmentation, and the selected product ion m/z signals are detected by the second mass analyser.

Peptide dereplication

Refers to the identification of known peptides in a sample by comparing mass spectrometric data with a library. The identification can be obtained by comparison of m/z mass signals, including the isotopologue intensities and pattern of isotopologues, giving information on the chemical composition as well as on tandem mass spectrometry (MS/MS) fragmentation spectra match with library data.

Peptide spectrum match

(PSM). A scoring function in which the mass spectrum of a peptide is compared with a theoretical peptide sequence to determine the probability of the measured peptide matching the theoretical peptide.

Post-source decay

A type of fragmentation technique that applies when metastable ions spontaneously decompose in the drift region between the ion source and reflectron.

Short open reading frames

(sORFs). Open reading frames that occur throughout the genome and usually comprise <100 codons. They are a possible source for peptides with biological relevance.

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Hellinger, R., Sigurdsson, A., Wu, W. et al. Peptidomics. Nat Rev Methods Primers 3, 25 (2023). https://doi.org/10.1038/s43586-023-00205-2

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