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Decoding the Mitochondrial Microproteome: proteomics strategies for Identifying Mitochondrial-derived Peptides

Peptidomics and small proteins Other

Abstract #272 Posted on28 March 202525 April 2025 25 April 2025 10h52

Author(s)

Anna Percio (Presenting Author) | Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore | Largo F. Vito,1, 00168, Rome, Italy
Federico Parisella | Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore | Largo F. Vito,1, 00168, Rome, Italy
Michela Cicchinelli | Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore | Largo F. Vito,1, 00168, Rome, Italy
Victor Corasolla Carregari | Department of Laboratory Diagnostic and Infectious Diseases, Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Fondazione Policlinico Universitario Agostino Gemelli-IRCCS | Largo Agostino Gemelli, 1, 00168, Rome, Italy
Elisabetta Betterini | Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore | Largo F. Vito, 1, 00168, Rome, Italy
Matteo Bordi | Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore | Largo F. Vito,1, 00168, Rome, Italy
Francesco Cecconi | Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore | Largo F. Vito, 1, 00168, Rome, Italy
andrea urbani | Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore | Largo F. Vito, 1, 00168, Rome, Italy
Viviana Greco | Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore | Largo F. Vito, 1, 00168, Rome, Italy

Abstract

Mitochondrial-derived peptides (MDPs), such as Humanin (HN), Humanin-like proteins and Mitochondrial open reading frame of the 12S rRNA (MOTS-c), are bioactive molecules encoded by small open reading frames within the 16S and 12S rRNA regions of mitochondrial DNA.
These peptides play key roles in metabolism, and aging, acting as retrograde signaling molecules regulating mitochondrial homeostasis.
Despite advances in proteomics, endogenous HN and MOTS-c (PE1) as well as Humanin-like proteins (PE2) remain undetected in standard datasets. This raises questions about methodological limitations and detection biases.
Within the Mitochondrial Human Proteome Project (mt-HPP) framework, this study aims to systematically investigate the endogenous presence of MDPs using publicly available datasets and newly acquired proteomics data. Combining different proteolytic digestions (trypsin, Glu-C, Lys-C), cytosolic and mitochondrial-enriched fractions from different cell lines (e.g. Hela, HEK293) were analyzed on Orbitrap Fusion Lumos Tribrid Mass Spectrometer (Thermo Scientific). Protein identification was performed by PeaksX software against high-accuracy databases searches (UniProt, MitoCarta, and a custom database); targeted peptides validation was conducted by Skyline.
By refining proteomic workflows, we aim to overcome detection challenges and enhance the MDPs identification, providing insights into their roles and potential implications in metabolic and neurodegenerative diseases.

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Mitochondrial-derived peptides (MDPs), such as Humanin (HN), Humanin-like proteins and Mitochondrial open reading frame of the 12S rRNA (MOTS-c), are bioactive molecules encoded by small open reading frames within the 16S and 12S rRNA regions of mitochondrial DNA. 
These peptides play key roles in metabolism, and aging, acting as retrograde signaling molecules regulating mitochondrial homeostasis.
Despite advances in proteomics, endogenous HN and MOTS-c (PE1) as well as Humanin-like proteins (PE2) remain undetected in standard datasets. This raises questions about methodological limitations and detection biases. 
Within the Mitochondrial Human Proteome Project (mt-HPP) framework, this study aims to systematically investigate the endogenous presence of MDPs using publicly available datasets and newly acquired proteomics data.  Combining different proteolytic digestions (trypsin, Glu-C, Lys-C), cytosolic and mitochondrial-enriched fractions from different cell lines (e.g. Hela, HEK293) were analyzed on Orbitrap Fusion Lumos Tribrid Mass Spectrometer (Thermo Scientific). Protein identification was performed by PeaksX software against high-accuracy databases searches (UniProt, MitoCarta, and a custom database); targeted peptides validation was conducted by Skyline.
By refining proteomic workflows, we aim to overcome detection challenges and enhance the MDPs identification, providing insights into their roles and potential implications in metabolic and neurodegenerative diseases.

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