{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Msf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/JAL_GSB_AH_MSRR_202109_TMT2_Fr4.msf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/JAL_GSB_AH_MSRR_202109_TMT2_Fr2.msf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/TMT1_heart.msf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/TMT3_soleus.msf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/TMT4_tibialis.msf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/JAL_GSB_AH_MSRR_202109_TMT2_Fr3.msf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/JAL_GSB_AH_MSRR_202109_TMT2_Fr5.msf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/JAL_GSB_AH_MSRR_202109_TMT2_Fr1.msf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/TMT2_diaphr.msf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/JAL_GSB_AH_MSRR_202109_TMT2_FrAll.msf"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/JAL_GSB_AH_MSRR_202109_TMT2_Fr3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/JAL_GSB_AH_MSRR_202109_TMT2_Fr2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/JAL_GSB_AH_MSRR_202109_TMT2_Fr5.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/TMT2_diaphr.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/TMT4_tibialis.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/JAL_GSB_AH_MSRR_202109_TMT2_FrAll.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/JAL_GSB_AH_MSRR_202109_TMT2_Fr4.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/TMT1_heart.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/JAL_GSB_AH_MSRR_202109_TMT2_Fr1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053573/TMT3_soleus.raw"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["ecalvo@cnic.es"],"submitter":["Enrique Calvo"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["","Mitochondria","Macrophage"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD053573"],"tissue":["Heart","Diaphragm"],"sample_protocol":["Labelled peptides were loaded in buffer A (0.1% of formic acid in water (v/v)) onto a C-18 reversed phase nano-column (75 μm I.D. and 50 cm, Acclaim PepMap) and separated in a continuous acetonitrile gradient consisting of 8-31% B-solution (0.1% formic acid (v/v) in acetonitrile) for 240 min, and 50-90% B for 1 min, at a flow rate of ~200 nL/min, using an UPLC-Ultimate 3000 chromatography system (Thermo Fisher, San José, CA, USA) connected to a Q-Exactive HF mass spectrometer (Thermo Fisher)."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["For peptide identification, MS/MS spectra were searched using the SEQUEST HT algorithm implemented in Proteome Discoverer 2.1 (Thermo Scientific) [1] against a Swiss-Prot [2] database comprising mouse protein sequences (mouse_202105_sw.target-decoy.fasta, 185234 sequences in total) concatenated with decoy sequences generated using DecoyPyrat [3]. Trypsin digestion was set with a maximum of 2 missed cleavages. Cys carbamidomethylation (57.021464 Da) and TMT labeling at the N-terminal end and Lys (229.162932 Da) were set as fixed modifications, and Met oxidation (15.994915 Da) as dynamic modification. Precursor mass tolerance was set at 800 ppm, fragment mass tolerance at 0.03 Da and precursor charge range to 2-4. The false discovery rate (FDR) was calculated using the corrected Xcorr score (cXcorr) [4] and the target/decoy competition strategy applying the picked FDR method at the peptide level [5], with an additional filter for precursor mass tolerance of 15 ppm [6]. A 1% FDR was employed as the criterion for peptide identification. [1] Orsburn BC. Proteome Discoverer-A Community Enhanced Data Processing Suite for Protein Informatics. Proteomes. 2021;9(1). [2] UniProt C. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Res. 2023;51(D1):D523-D31. [3] Wright JC, Choudhary JS. DecoyPyrat: Fast Non-redundant Hybrid Decoy Sequence Generation for Large Scale Proteomics. J Proteomics Bioinform. 2016;9(6):176-80. [4] Keller A, Nesvizhskii AI, Kolker E, Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem. 2002;74(20):5383-92. [5] Prieto G, Vazquez J. Protein Probability Model for High-Throughput Protein Identification by Mass Spectrometry-Based Proteomics. J Proteome Res. 2020;19(3):1285-97. [6] Bonzon-Kulichenko E, Garcia-Marques F, Trevisan-Herraz M, Vazquez J. Revisiting peptide identification by high-accuracy mass spectrometry: problems associated with the use of narrow mass precursor windows. J Proteome Res. 2015;14(2):700-10."],"omics_type":["Proteomics"],"labhead":["Enrique Calvo"],"instrument_platform":[""],"labhead_affiliation":["CNIC"],"submission_type":["PARTIAL"],"species":["Mus Musculus (mouse)"],"submitter_mail":["ecalvo@cnic.es"],"publication":["Not available"],"submitter_affiliation":["CNIC"],"submitter_country":["Spain"],"additional_accession":[]},"is_claimable":false,"name":"Mitochondria facilitate their own removal by expanding the macrophage pool","description":"Specialized tissues demand support for long-term fitness. In the heart, for example, the removal of spent mitochondria by macrophages is critical for cardiac function. In an organismal-wide screening, we show here that the transfer of mitochondria to macrophages is prominent in other organs that rely on mitochondrial respiration, including the skeletal muscle and brown adipose tissue (BAT). Depletion of macrophages altered the mitochondrial activity and compromised the mechanical and thermogenic performance of these organs. Using comparative, genetic and surgical approaches, we show that the abundance of macrophages in a muscle is dictated by the mitochondrial activity of its myofibers, and that this is achieved by modulating the number of Csf1-producing fibroblasts in the tissue. Consequently, inhibition of the Csf1 receptor collapsed the mitochondrial activity of skeletal muscles. Thus, by regulating the abundance of macrophages, tissues enact an adaptive mechanism that copes with high mitochondrial turnover and supports their 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