{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD061150/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD061150/S16825_378_Lilian_IP_1_240610.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD061150/S16830_383_Lilian_IP_6_240610.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD061150/S16829_382_Lilian_IP_5_240610.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD061150/S16828_381_Lilian_IP_4_240610.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD061150/S16827_380_Lilian_IP_3_240610.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD061150/S16826_379_Lilian_IP_2_240610.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD061150/Proteomics.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["antoine.dufour@ucalgary.ca"],"submitter":["Daniel Young"],"technology_type":["Mass Spectrometry","Bottom-up proteomics","Data-independent acquisition"],"software":[""],"submitter_keywords":["Mouse","Granules","Mast cell"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD061150"],"tissue":["Peritoneal Fluid"],"sample_protocol":["Peritoneal mast cells were sorted and then stimulated with either ATP and Ca2+ or by sonication. Following stimulation, the cell suspension was incubated with Avidin TR (Avidin suforhodamine 101, Abcam, #275308) at a concentration of 0.3 μg/ml for 10 minutes. The suspension was then centrifuged at 350 g for 5 minutes at 4°C to pellet the cells and remove debris. The supernatant was transferred to a new 2 ml Eppendorf tube and centrifuged at 14,000 g for 5 minutes. After centrifugation, the supernatant was discarded, and the pelleted mast cell granules were resuspended with Biotin magnetic beads (Ray-Biotech, #801-107). Finally, the granules were isolated using a magnetic sorting technique.   Mast cell granules were isolated and prepared through sonication and stimulation with Ca²⁺ and ATP, as described before. The samples were collected in three biological replicates. 50% trichloroacetic acid (TCA) was used for protein precipitation and incubated overnight at -20°C. The samples were centrifuged at 14,000 x g for 10 minutes to pellet the proteins. The supernatant was carefully discarded, and the remaining pellet was washed 3 times with cold acetone. After each wash, samples were centrifuged again at 14,000 x g for 10 minutes, and the supernatant was discarded. The protein pellet was resuspended in 230 µl Urea/Tris buffer in a shaker for 20 minutes at room temperature (RT) until the pellet was dissolved. Reduction was performed using 10 mM dithiothreitol (DTT) at 37°C for 30 minutes, then transferred into a 30 kDa Amicon spin column. Proteins were then alkylated with 10 mM iodoacetamide (IAA) prepared in Urea-Tris and incubated in the dark at RT for 20 minutes. A centrifuge at 14,000 x g for 10 minutes was used to discard the supernatant. Afterward, three sequential washes were done with urea-Tris and three washes in 50 mM ammonium bicarbonate; samples underwent overnight trypsin digestion with a 1:10 trypsin: total protein ratio. The following day,  50 mM ammonium bicarbonate was added to the samples, incubated for 3-5 minutes, and then centrifuged at 14,000 x g for 10 minutes. The collected liquid was set to pH< 3 and desalted using buffers and C18 Sep-Pak columns (Waters, Mississauga, ON, Canada). The peptides were dried using a SpeedVac and analyzed using liquid chromatography and tandem mass spectrometry (LC-MS/MS)"],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":[". Data-independent acquisition by Neural Networks, which is a software developed to process large-scale protein data (DIA-NN, version 1.8.1), was employed to apply a library-free search on DIA raw files and obtained spectra to match with the UniProt mouse protein reference proteome.   MSstats (v4.10.1), MSstats TMT (v2.10.0), and MSstatsPTM (v2.4.4) packages installed in R (v4.4.0) were used to analyze the raw data obtained from DIA_NN software. Protein quantification and normalization were performed using the MSstats::dataProcess() function. The data was normalized using the 'equalizeMedians' method and log2-transformed."],"omics_type":["Proteomics"],"labhead":["Antoine Dufour"],"instrument_platform":[""],"labhead_affiliation":["Physiology & Pharmacology, Cumming School of Medicine, University of calgary, Cagary"],"submission_type":["PARTIAL"],"species":["Mus Musculus (mouse)"],"publication":["Not available"],"submitter_mail":["daniel.young1@ucalgary.ca"],"submitter_affiliation":["University of Calgary"],"submitter_country":["Canada"],"additional_accession":[]},"is_claimable":false,"name":"A Nerve and Mast Cell Sentinel System Releases Extracellular Condensates to Induce Macrophage Repair","description":"The peritoneal cavity has a higher density of immune cells then does blood. These cells are primarily localized within the bulk flow of fluid. As such, any perturbation within the peritoneum, ranging from a sterile injury to endometriosis to ovarian cancer, requires that the immune cells find a way to recognize and nucleate at the site. Due to the very stochastic nature of the bulk flow within the peritoneal cavity, chemotactic gradients are unlikely to form and immune cell recruitment almost certainly requires a series of molecular events unlike in any other compartment. Herein, without breaching the peritoneal cavity we induced a laser injury, killing approximately a hundred mesothelial cells and used a two-photon microscope that could image through the abdominal wall to observe a spectacular accumulation of large peritoneal macrophages at the injury site. Large (1 μm) condensates (membraneless organelles) were released from mast cells due to sensory neuron activation and substance P release. The condensates expressed the scavenger receptor MARCO and harbored more than 200 different proteins. They were stable in extracellular fluid and highly adhesive causing macrophages to aggregate, nucleate and become M2-like at the injury site. Lattice light sheet microscopy unveiled mast cells to have very thin (<10nm) tentacle like filapodia (arms) that were often hundreds of microns in length, motile and grabbed the condensates from the mast cell surface and deposited them on neighboring cells thereby regulating the sphere of influence of each individual mast cell.","dates":{"publication":"2026-06-17","submission":"2025-02-24"},"accession":"PXD061150","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","NEWT:35554","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:32049","NEWT:1392696","NEWT:259447","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:180454","NEWT:5722","NCBITaxon:1280","NEWT:1129","NEWT:55153","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:10036","NEWT:1590","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:1147161","NEWT:224326","NEWT:1333499","NCBITaxon:79857","NEWT:1096976","NEWT:95648","NEWT:1589","NEWT:135622","NEWT:1349","NEWT:96731","NEWT:383379","NEWT:10029","NEWT:913645","NEWT:44491","NEWT:556484","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:3112","NEWT:4442","NEWT:192875","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:108061","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:931281","NEWT:658457","NEWT:77133","NEWT:295358","NEWT:145481","NCBITaxon:79824","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:44447","NEWT:5759","NEWT:1736231","NEWT:1392","NEWT:498217","NEWT:2242","NEWT:11320","NEWT:286","NEWT:391619","NEWT:246196","NEWT:287","NEWT:246197","NEWT:633149","NEWT:10239","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:5507","NEWT:410661","NEWT:55571","NEWT:35500","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:4896","NEWT:1390","NEWT:11557","NEWT:1094343","NEWT:1336795","NEWT:644042","NEWT:294","NEWT:1773","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:935293","NEWT:375146","NEWT:118698","NEWT:263","NEWT:118696","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44664","NEWT:47946","NEWT:3702","NEWT:243277","NEWT:7067","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:33548","NEWT:274","NEWT:408172","NEWT:408170","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:1436733","NEWT:460519","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:9483","NEWT:1513458","NCBITaxon:40559","NEWT:84588","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:508771","NEWT:1883446","NEWT:253","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:93062","NCBITaxon:4932","NEWT:644223","NEWT:235443","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:320637","NEWT:983964","NEWT:118499","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:3988","NEWT:1255228","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:39491","NCBITaxon:5811","NEWT:29491","NEWT:2014887","NEWT:33952","NEWT:261756","NEWT:571256","NEWT:40483","NEWT:272634","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:141262","NEWT:108931","NEWT:1055524","NEWT:4087","NEWT:9778","NEWT:306","NEWT:150475","NEWT:303","NEWT:267872","NEWT:7111","NEWT:347515","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:4090","NEWT:4092","NEWT:9541","NEWT:4093","NEWT:4096","NEWT:185579","NEWT:941442","NEWT:13076","NEWT:7108","NEWT:40479","NEWT:4076","NEWT:317","NEWT:1006581","NEWT:885318","NEWT:39488","NEWT:550","NEWT:4081","NEWT:273068","NEWT:554","NEWT:98334","NEWT:451516","NEWT:36185","NEWT:1225786","NEWT:7574","NEWT:1715256","NEWT:30640","NEWT:575412","NEWT:929793","NEWT:29204","NEWT:28112","NEWT:114155","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:6239","NEWT:162425","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:1268063","NEWT:1263854","NEWT:118503","NEWT:2059687","NEWT:160488","NEWT:28104","NEWT:407821","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:986","NEWT:52641","NEWT:7159","NEWT:28532","NEWT:353152","NEWT:8496","NEWT:27448","NEWT:1194669","NEWT:51329","NEWT:243230","NEWT:1080772","NEWT:519","NEWT:8479","NEWT:8485","NEWT:6063","NEWT:49240","NEWT:104395","NEWT:6289","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:469008","NEWT:256318","NEWT:9321","NEWT:206411","NCBITaxon:6191","NEWT:596153","NEWT:229533","NEWT:1836","NEWT:80863","NEWT:105231","NEWT:52638","NEWT:57075","NEWT:4097","NEWT:884204","NEWT:9785","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","NEWT:83906","NCBITaxon:780","NCBITaxon:1502","NEWT:6282","NEWT:1134506","NEWT:38783","NEWT:4006","NEWT:6426","NCBITaxon:5476","NEWT:6669","NEWT:9935","NEWT:89453","NEWT:287889","NEWT:51515","NEWT:588596","NEWT:51511","NEWT:8845","NEWT:92867","NEWT:92866","NEWT:5334","NEWT:51750","NEWT:202950","NEWT:382352","NEWT:413071","NEWT:632957","NEWT:9925","NEWT:89462","NEWT:8839","NEWT:90690","NEWT:4232","NEWT:2758385","NEWT:11298","NEWT:171101","NEWT:714","NEWT:421932","NEWT:312017","NEWT:196627","NEWT:200308","NEWT:200302","NEWT:870435","NEWT:284593","NEWT:100392","NEWT:5315","NEWT:9913","NEWT:265872","NEWT:105841","NEWT:337330","NEWT:2666255","NEWT:2285","NEWT:999810","NCBI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