{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Msf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063777/YandongZhang10461950_YDZ_01262023_MMFynepprofiling_2.msf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063777/YandongZhang10461950_YDZ_01262023_MMFynepprofiling_r.msf"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063777/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063777/YandongZhang10461950_YDZ_01262023_MMFynepprofiling_r.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063777/YandongZhang10461950_YDZ_01262023_MMFynepprofiling_2.raw"],"Mgf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063777/YandongZhang10461950_YDZ_01262023_MMFynepprofiling_2.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063777/YandongZhang10461950_YDZ_01262023_MMFynepprofiling_r.mgf"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["qf44@cornell.edu"],"submitter":["Qin Fu"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Dimethyl fumarate","Macrophage"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD063777"],"tissue":["Cell Culture","Fibroblast"],"sample_protocol":["Following LPS stimulation, the macrophages were treated with MMFyne or DMF (negative control) for one hour and then collected and lysed the cells. Subsequently, the MMFyne-modified proteins were labeled with biotin-azide via click chemistry. Then the labeled proteins were enriched using streptavidin beads. The enriched proteins were subjected to on-beads trypsin digestion and the resulting peptides from MMFyne and DMF treated samples were labeled with heavy or light dimethyl labeling, enabling their identification and quantification via LC-MS."],"repository":["Pride"],"modification":[""],"quantification_method":[""],"data_protocol":["The raw files were searched by Proteome Discoverer 2.5 against Mus musculus Uniprot database which has 17114 sequences. Oxidation of M, deamidation of N and Q, dimethyl light(28.031Da) and heavy (32.056Da) labeling on K and peptide N-terminal were specified as dynamic modifications; protein N-terminal acetylation, M-loss, M-loss+acetylation were set as a variable modification;  carbamidomethyl C was specified as a static modification."],"omics_type":["Proteomics"],"labhead":["Qin Fu"],"instrument_platform":[""],"labhead_affiliation":["Cornell University"],"species":["Homo Sapiens (human)"],"submission_type":["PARTIAL"],"publication":["42019494 Zhang Y, Lindner H, So B, Chen Z, Li H, Xu J, Wang J, Xu J, Petre AM, Distefano MD, Núñez G, Lin H. NEK7 Cys298 is important for NLRP3 inflammasome and targetable by dimethyl fumarate. Cell Chem Biol. 2026 33(5):711-719.e4 10.1016/j.chembiol.2026.03.016"],"submitter_mail":["qf44@cornell.edu"],"submitter_affiliation":["Cornell University"],"submitter_country":["United States"],"pubmed_abstract":["Dimethyl fumarate (DMF), a cysteine targeting agent, is clinically used to treat multiple sclerosis and psoriasis. However, its precise molecular mechanism remains incompletely understood. Here, we investigated the effects of DMF on NLRP3 inflammasome activation. DMF suppresses NLRP3 inflammasome activity at both the priming and activation steps. Using chemoproteomics, we identified DMF targets in macrophages, including IRAK3/4 and RELA/B involved in the NLRP3 priming step, NEK7 involved in NLRP3 early activation, and GSDMD involved in NLRP3 late activation. To understand how DMF inhibits NLRP3 early activation, we showed that DMF modifies NEK7 Cys298 to disrupt NLRP3-NEK7 interaction and inflammasome activation. Interestingly, NEK7 Cys298 is critical for NLRP3 inflammasome activation. This study provides mechanistic insights into DMF's immunomodulatory effects and suggests that targeting NEK7 Cys298 can be a novel strategy for inflammatory diseases. Our work highlights the utility of DMF to identify functionally important cysteine residues in immune signaling pathways."],"pubmed_title":["NEK7 Cys298 is important for NLRP3 inflammasome and targetable by dimethyl fumarate."],"pubmed_authors":["Zhang Yandong Y, Lindner Helena H, So Brian B, Chen Zirong Z, Li Haoyang H, Xu Jiashu J, Wang Jiahe J, Xu Jie J, Petre Alexandru M AM, Distefano Mark D MD, Núñez Gabriel G, Lin Hening H"],"additional_accession":[]},"is_claimable":false,"name":"Dimethyl fumarate targets in macrophages","description":"To understand the molecular mechanism underlying DMF’s inhibition of NLRP3 inflammasome in macrophage, we conducted chemoproteomics to identify the specific protein targets of DMF. We used MMFyne, a previously reported clickable DMF analogue to label and help identify potential DMF target proteins in macrophages.","dates":{"publication":"2026-05-25","submission":"2025-05-08"},"accession":"PXD063777","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:309807","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:1214915","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:108061","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:931281","NEWT:658457","NEWT:1310161","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: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","NCBITaxon:9606","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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