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Cornett"],"technology_type":["Data-dependent acquisition","Mass Spectrometry"],"software":["Not available"],"submitter_keywords":["Lysine methylation","Neuronal differentiation","Luhmes"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD069591"],"tissue":["Neuronal Cell Line"],"sample_protocol":["LUHMES cells were collected for mass spectrometry analysis on differentiation days 0, 2, and 6 (n=4 biological replicates per time point). Cell pellets were resuspended in 400 µL 8 M Urea, 100 mM Tris pH 8.5 and transferred to Diagenode Bioruptor tubes (Cat No: C30010010). Cells were lysed via Diagenode Bioruptor, 30s on/30s off, for 30 cycles. Samples were then clarified, and protein concentration determined by Bradford assay(Biorad Cat No# 500201 ). 25 µg of each sample was treated with five mM tris(2-carboxyethyl)phosphine hydrochloride (TCEP, Sigma-Aldrich Cat No: C4706) to reduce disulfide bonds and the resulting free cysteine thiols were alkylated with 10 mM chloroacetamide (CAA, Sigma Aldrich Cat No: C0267). Samples were diluted with 50 mM Tris.HCl pH 8.5 (Sigma-Aldrich Cat No: 10812846001) to a final urea concentration of 2 M for overnight Trypsin / Lys-C digestion at 35 ºC (1:50 protease: substrate ratio, Mass Spectrometry grade, Promega Corporation, Cat No: V5072). In addition to the 12 samples that were digested with Trypsin/LysC, 12 samples were reduced and alkylated as stated above, then diluted to <0.5 M Urea with 100 mM Tris-HCl and 10 mM CaCl2, pH 7.8, and digested with Chymotrypsin overnight at 35 ºC (1:25 protease: substrate, Roche Cat no: 11418467001). Digestions were quenched with trifluoroacetic acid (TFA, 0.5% v/v) and desalted on Waters Sep-Pak® Vac cartridges (Waters™ Cat No: WAT054955) with a wash of 1 mL 0.1% TFA followed by elution in 0.6 mL of 70% acetonitrile 0.1% formic acid (FA). Peptides were dried by speed vacuum and resuspended in 50 mM triethylammonium bicarbonate. Samples were divided into two 12-plex samples. Each sample was then labeled for overnight at room temperature, with 0.5 mg of Tandem Mass Tag Pro (TMTpro) reagent (16-plex kit, manufacturer’s instructions, Thermo Fisher Scientific, TMTpro™ Isobaric Label Reagent Set; Cat No: 44520, lot no. ZA382395. Prior to quenching, labeling efficiency of over 95% was confirmed. Reactions were quenched with 0.3 % hydroxylamine (v/v) at room temperature for 15 minutes. Labeled peptides were then mixed and dried by speed vacuum. The Chymotrypsin 12-plex resuspended in 0.5% TFA and fractionated on a Waters Sep-Pak® Vac cartridge (Waters™ Cat No: WAT054955) with a 1 mL wash of water, 1 mL wash of 5% acetonitrile, 0.1% triethylamine (TEA) followed by elution in 12.5%, 15%, 17.5%, 20%, 22.5%, 25%, 30%, and 70% acetonitrile, all with 0.1% TEA). The Trypsin / Lys-C 12-plex was resuspended in 10 mM ammonium formate, pH 10 half of each mix was fractionated using an offline Thermo UltiMate 3000 HPLC with a Waters Xbridge C18 column (3.5 µm x 4.6mm x 250 mm, Cat No: 186003943; Buffer A: 10 mM formate pH 10, Buffer B: 10 mM formate pH 10, 95% acetonitrile, gradient 1 mL/min 0-15%B over 5 min, 15-20% B over 5 min, 20-35%B over 75 min, 35-50% B over 5 min, 50-60% B over 10 min and a 6 minute hold at 60% B). Fractions were collected continuously every 60 seconds into 9- well plates. Initial and late fractions with minimal material were combined and lyophilized. The remaining fractions were concatenated into 24 fractions, dried down, and resuspended in 50 µL 0.1% FA prior to online LC-MS34,35 .   Mass spectrometry was performed utilizing an EASY-nLC 1200 HPLC system (SCR: 014993, Thermo Fisher Scientific) coupled to Orbitrap Fusion Eclipse mass spectrometer (Thermo Fisher Scientific) with FAIMSpro interface (Thermo Fisher Scientific). Each multiplex was run on an Aurora column with 180-minute gradient. For each fraction, 25% of the sample was loaded onto an Aurora column, and run at a flow rate of 350 nl/min. (Thermo Fisher ES902) The gradient (Mobile phases A: 0.1% formic acid (FA), water; B: 0.1% FA, 80% Acetonitrile (Thermo Fisher Scientific Cat No: LS122500)), was increased from 8-38%B over 160 minutes; 95% B over 12 mins; and dropping from 95%-5% B over the final 8 min. The mass spectrometer was operated in positive ion mode, default charge state of 2, advanced peak determination on, and Easy IC™ switched to on. Three FAIMS CVs were utilized (-45 CV; -55 CV; -65CV) each with a cycle time of 1 s and with identical MS and MS2 parameters. Precursor scans (m/z 400-1600) were done with an orbitrap resolution of 120000, RF lens% 30, dynamic maximum inject time, standard AGC target, minimum MS2 intensity threshold of 2.5 e4, MIPS mode to peptide, including charges of 2 to 7 for fragmentation with 60 sec dynamic exclusion. MS2 scans were performed with a quadrupole isolation window of 0.7 m/z, 34% HCD CE, 15000 resolution, standard AGC target, automatic maximum IT, fixed first mass of 100 m/z."],"repository":["Pride"],"quantification_method":[""],"modification":["","N6"],"data_protocol":["Resulting RAW files were analyzed in Proteome Discover™ 2.5 (Thermo Fisher Scientific) with a Homo sapiens UniProt reviewed proteome FASTA (downloaded 05/13/22, 20,282 sequences) plus common laboratory contaminants (73). SEQUEST HT searches were conducted with full trypsin digest, 5 maximum number missed cleavages; precursor mass tolerance of 10 ppm; and a fragment mass tolerance of 0.02 Da. Static modifications used for the search were: 1) carbamidomethylation on cysteine (C) residues; 2) TMTpro label on N-termini of peptides. Dynamic modifications used for the search were 1) TMTpro label on lysine (K) residues, 2) methylation on lysine (K) residues, 3) dimethylation on lysine (K) residues, 4) trimethylation on lysine (K) residues, 5) oxidation of methionines, 6) methionine loss or acetylation with methionine loss on protein N-termini. A maximum of 5 PTMs was allowed per peptide. The same parameters were used for the Chymotrypsin digest except use of Chymotrypsin as the protease. Percolator False Discovery Rate was set to a strict setting of 0.01 and a relaxed setting of 0.05. IMP-ptm-RS node was used to calculate modification site localization scores. Values from both unique and razor peptides were used for quantification. In the consensus workflows, peptides were normalized by total peptide amount with no scaling. Quantification methods utilized TMTpro isotopic impurity levels available from Thermo Fisher Scientific. Reporter ion quantification used a minimum S/N threshold of 6 and co-isolation values of equal to or less than 30%. Resulting grouped abundance values for each sample type, abundance ratio values; and respective p-values (t-test) from Proteome Discover were exported to Microsoft Excel."],"omics_type":["Proteomics"],"labhead":["Evan Cornett"],"instrument_platform":[""],"submission_type":["COMPLETE"],"labhead_affiliation":["Department of Biochemistry, Molecular Biology and Pharmacology, Indiana University School of Medicine, USA"],"species":["Homo Sapiens (human)"],"publication":["Not available"],"submitter_mail":["evcorn@iu.edu"],"submitter_affiliation":["Indiana University School of Medicine"],"submitter_country":["United States"],"doi":["10.6019/PXD069591"],"additional_accession":[]},"is_claimable":false,"name":"Characterization of Non-histone Lysine Methylation Across Neuronal Differentiation of LUHMES","description":"Over one-third of human lysine methyltransferases (KMTs) and lysine demethylases (KDMs), the enzymes responsible for adding or removing methylation on lysine residues within proteins, are linked to neurodevelopmental disorders (NDDs). Consequently, several studies have explored the roles of specific KMTs or KDMs in neuronal differentiation, and alterations in histone methylation patterns have been identified. However, it is now widely recognized that KMTs and KDMs also target non-histone proteins, yet knowledge of how non-histone lysine methylation changes during neuronal differentiation remains limited. Here, we address this gap using quantitative mass spectrometry-based proteomics to identify and measure changes in non-histone lysine methylation at three different stages in the Lund human mesencephalic (LUHMES) neuronal differentiation model. We identify 74 lysine methylation sites with significant differences in abundance across differentiation. Our analysis reveals lysine methylation on many non-histone proteins involved in neuronal differentiation and neurodevelopment, including signaling molecules, cytoskeletal proteins, RNA splicing factors, and transcription factors. Overall, this work broadens the understanding of non-histone lysine methylation in a neuronal differentiation model and offers a valuable resource of lysine methylation sites on proteins of biological and clinical significance for future research.","dates":{"publication":"2026-10-02","submission":"2025-10-17"},"accession":"PXD069591","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:6819","NEWT:475174","NEWT:111205","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:10034","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:1589","NEWT:135622","NEWT:67352","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:36630","NEWT:383379","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:111225","NEWT:7719","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:3347","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:410658","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:44685","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:28174","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:244366","NEWT:1246791","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:33995","NEWT:55784","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2853422","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:95486","NEWT:1883446","NEWT:1233435","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:491","NEWT:460523","NEWT:235443","NEWT:1757312","NEWT:85694","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:373153","NEWT:472","NEWT:940825","NEWT:529507","NEWT:1071661","NEWT:470","NEWT:5911","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:906914","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:51338","NEWT:575412","NEWT:28112","NEWT:6493","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:5147","NEWT:28108","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:298176","NEWT:227377","NEWT:1774284","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:443906","NEWT:519","NEWT:2510939","NEWT:7394","NEWT:6063","NEWT:1328388","NEWT:105487","NEWT:1548728","NEWT:667127","NEWT:9557","NEWT:377586","NEWT:7375","NEWT:300641","NEWT:39655","NEWT:9554","NEWT:38323","NEWT:475932","NEWT:256318","NEWT:206411","NCBITaxon:6191","NEWT:229533","NEWT:2925","NEWT:214053","NEWT:28550","NEWT:80863","NEWT:90675","NEWT:52638","NEWT:57075","NEWT:1666905","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:1123869","NEWT:9544","NEWT:9545","NEWT:979","NEWT:7370","NEWT:83906","NEWT:99488","NEWT:1134506","NEWT:255470","NEWT:38783","NEWT:6426","NEWT:33090","NEWT:9935","NEWT:287889","NEWT:305959","NEWT:13489","NEWT:29829","NEWT:92867","NEWT:92866","NCBITaxon:3055","NEWT:51750","NEWT:202950","NEWT:441772","NEWT:48106","NEWT:295027","NCBITaxon:11320","NEWT:632957","NEWT:9925","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