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PXD026317/Lumos1_LOS_Set2_IMAC-TMT_P11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set4_IMAC-TMT_A5R.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set4_IMAC-TMT_E4R.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos1_LOS_set1_IMAC-TMT_P10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set3_IMAC-TMT_D6R.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos1_LOS_set3_IMAC-TMT_D4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set6_FullProt-P11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos1_LOS_set1_IMAC-TMT_A5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set3_IMAC-TMT_A5R.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set4_IMAC-TMT_F3R.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set6_FullProt-C5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set5_FullProt-F4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set4_IMAC-TMT_P11R.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set4_IMAC-TMT_P06R.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos1_LOS_Set2_IMAC-TMT_A5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set4_IMAC-TMT_G5R.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos1_LOS_set1_IMAC-TMT_F3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set3_IMAC-TMT_P06R.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set5_FullProt-P03.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set6_FullProt-G5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos1_LOS_Set2_IMAC-TMT_D6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set3_IMAC-TMT_C6R.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set6_FullProt-E5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos1_LOS_Set2_IMAC-TMT_G4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set5_FullProt-H4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set3_IMAC-TMT_P11R.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos1_LOS_set1_IMAC-TMT_C5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set4_IMAC-TMT_P08R.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set6_FullProt-P06.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos1_LOS_set1_IMAC-TMT_P05.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set3_IMAC-TMT_F5R.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos1_LOS_Set2_IMAC-TMT_P06.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lumos3_LOS_Set5_FullProt-B5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/LOS_Set5_Set6_FullProt_TMT8plex_SNRatio.pdResultftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/Lourdes_IMAC-TMT10plex_all4sets_SNRatio.pdResultftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD026317/LOS_Set5_Set6_FullProt_TMT8plex_Intensity.pdResultprimaryOK200jyoti.choudhary@icr.ac.ukJames WrightMass SpectrometryShotgun proteomicsPhosphoproteom32dProteomeTmthttps://www.ebi.ac.uk/pride/archive/projects/PXD026317Cell CultureCell pellets were lysed in 5% SDS/100mM TEAB containing 2x of Halt™ Protease and Phosphatase Inhibitor® (Thermo Fisher) with probe sonication at 40% power, 10x 1s on/ 1s off.and heating, then were heated at 90⁰C for 10 min and probe sonicated again. Protein concentrations were measured by Pierce™ 660nm Protein Assay (Thermo Fisher). 300 µg of proteins were reduced by 20mM TCEP and alkylated by 20mM iodoacetamide, purified by chloroform/methanol precipitation, digested by Pierce™ Trypsin (MS grade, Thermo Fisher) at 37⁰C for 17 hours (trypsin : proteins = 1:30 (w:w)). The digestion were dried in SpeedVac, then redissolved in 50% acetonitrile/0.5% formic acid (FA) and SpeedVac dried again. Phosphopeptides enrichment used Phos-Select Affinity Gel (Sigma) as instructed by the manufacturer with minor modification, i.e. the IMAC binding and washing buffer were 0.1%TFA/250mM acetic acid/50% acetonitrile, and the elution used 150 µl of 1.5% NH4OH/100% H2O then 150 µl of 1.5% NH4OH/25% CH3CN. Enriched phosphopeptides were dried in SpeedVac twice as above. Peptides were labelled by TMT10plex (Thermo Fisher) as instructed by the manufacturer. Samples were mixed, dried in SpeedVac, and then were fractionated on an XBridge BEH C18 column (2.1 mm i.d. x 150 mm, Waters) with 5% ACN/0.1% NH4OH (pH 10) – 35% CH3CN /0.1% NH4OH in 30 min/total cycle 60min. The flow rate was at 200 µl/min. Fractions were collected ay every 30 sec and then concatenated to 34 fractions (phosphoproteome) or 24 fractions (full proteome) and dried in SpeedVac. The LC-MS/MS analysis were 2 hours for each fraction from 4-30% acetonitrile/0.1% FA for phosphopeptides or 8-30% acetonitrile/0.1% FA for full proteome samples. The MS full scan were at m/z 375 – 1500 with AGC at 4x 105 /50 msec. For phosphopeptides analysis, the MS2 detection was in Orbitrap, MS2 fragmentation was in HCD with 38% collision energy (CE). For full proteome, the MS2 fragmentation was in ion trap with CID with 35%CE, and the reporter ions were detected in MS3 level in Orbitrap with Synchronous Precursor Selection (SPS) method from the top 5 fragment ions with 65% CE.PrideThe raw files were processed in Proteome Discoverer 2.4 (Thermo Fisher) using the Sequest HT and Mascot search engines. Spectra were searched against fasta files of reviewed Uniprot Mus musculus entries (Januray 2021) and an in-house contaminate database. Search parameters were: trypsin with 2 maximum miss-cleavage sites, mass tolerances at 20 ppm for precursor, and 0.5 Da for fragment ions (full proteome) or 0.1 Da (for phosphoproteome), dynamic modifications of Deamidated (N, Q), Oxidation (M) and Acetyl (Protein N-term), static modifications of Carbamidomethyl (C) and TMT6plex (Peptide N-terminus and K). For phosphoproteome, phosphoryl (S,T,Y) was also set as dynamic modification. Peptides were validated by Percolator with q-value set at 0.01 (strict) and 0.05 (relaxed). Only unique peptides were used for quantification. The co-Isolation threshold was set at 100%. Peptides with average reported S/N>3 were used for protein quantification, and the SPS mass matches threshold was set at 50%. The abundance normalization mode used the total peptide amount, and scaling mode used on all average.ProteomicsJyoti ChoudharyThe Institute of Cancer ResearchPARTIALMus Musculus (mouse)james.wright@icr.ac.ukNot availableThe Institute of Cancer ResearchUnited KingdomfalseG-CSF mediated signalling in 32D cellsG-CSF signalling has been extensively characterized in myeloid progenitor cells but the activation dynamics downstream of the receptor at different stages of cell differentiation in wild-type G-CSFR or in proliferating cells that harbor the d715 mutation has not been been investigated at the phosphoproteome/proteome level. Proteome and phosphoproteome profiling using 10 plexTMT has been performed on 32D cells stimulated with G-CSF on d715 mutant cells, wild type cells on day 0, day 3 and day 6 of cell differentiation. Each sample on each day has 5 time points sampled at t=0,5,10,15,30 minutes post G-CSF stimulation.2026-06-222021-05-27PXD026317NEWT:6945NEWT:3555NEWT:241368NEWT:2NEWT:157546NEWT:42528NEWT:190802NEWT:35554NEWT:9778NEWT:150475NEWT:38942NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:307972NEWT:32046NEWT:544496NEWT:5180NEWT:256737NEWT:2042546NEWT:115104NEWT:1081927NEWT:1238993NEWT:67825NEWT:185579NEWT:43179NEWT:13076NEWT:4513NEWT:1249668NEWT:376741NEWT:317NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:7227NEWT:7469NEWT:885318NEWT:1211601NEWT:415540NEWT:876138NEWT:4081NEWT:554NEWT:98334NEWT:426428NEWT:237561NEWT:6928NEWT:10036NEWT:7574NEWT:1351NEWT:1438992NEWT:7215NEWT:2649997NEWT:575412NEWT:29204NEWT:272563NEWT:507601NCBITaxon:79857NCBITaxon:6157NEWT:95648NEWT:3885NEWT:746360NEWT:6239NEWT:3888NEWT:1589NEWT:470150NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:4054NEWT:3880NEWT:272559NEWT:226186NEWT:1268063NEWT:3641NEWT:383379NEWT:8782NEWT:1263854NEWT:10029NEWT:1000589NEWT:435590NEWT:1902NEWT:85962NEWT:160488NEWT:28104NEWT:317447NEWT:7955NCBITaxon:2NEWT:985076NEWT:7959NEWT:1215323NEWT:2261NEWT:4565NEWT:1264690NEWT:515619NEWT:6192NEWT:28532NCBITaxon:38727NEWT:192875NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:216599NEWT:139927NEWT:4558NEWT:209285NEWT:216595NEWT:243230NEWT:8355NEWT:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:9685NEWT:7029NEWT:1283300NEWT:6183NEWT:6063NEWT:334747NEWT:61235NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:3218NEWT:5759NEWT:1736231NEWT:6289NEWT:436486NEWT:6287NEWT:2242NEWT:300641NEWT:4784NEWT:727NEWT:9796NEWT:11320NEWT:725NEWT:360106NEWT:260707NEWT:287NEWT:10117NEWT:10239NCBITaxon:6191NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:83334NEWT:185431NEWT:83332NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:44685NEWT:2697049NEWT:1148NEWT:580240NEWT:11676NEWT:55571NEWT:100226NCBITaxon:6073NEWT:884204NEWT:4530NEWT:4896NEWT:6279NEWT:1123869NEWT:9544NEWT:7370NEWT:75058NEWT:83906NEWT:607699NEWT:13616NEWT:6282NEWT:1094343NEWT:208964NEWT:1134506NEWT:575584NEWT:296543NEWT:1773NEWT:38783NEWT:8727NEWT:1895NEWT:4006NEWT:1182590NEWT:8726NEWT:6426NEWT:6669NEWT:10090NEWT:935293NEWT:64152NEWT:749200NEWT:4120NEWT:51515NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:990346NEWT:5334NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:284812NCBITaxon:10359NCBITaxon:1313NEWT:43330NEWT:242619NEWT:44544NEWT:632957NEWT:373995NEWT:5689NEWT:645463NEWT:544404NEWT:3702NEWT:129249NEWT:9925NEWT:8839NEWT:4232NEWT:990119NEWT:2758385NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:714NEWT:421932NEWT:196627NEWT:408172NEWT:5691NEWT:408170NEWT:493760NEWT:260710NEWT:627025NEWT:257313NEWT:400772NEWT:1097677NEWT:3708NEWT:128161NEWT:332648NEWT:106592NEWT:536231NEWT:61674NEWT:1117957NEWT:9913NEWT:1432138NEWT:10312NEWT:1424507NCBITaxon:1773NEWT:4100NEWT:1076NEWT:9598NEWT:6763NEWT:803NEWT:8030NEWT:29722NEWT:380394NEWT:1692259NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:180066NEWT:67767NEWT:46835NEWT:135588NEWT:376686NEWT:1843183NEWT:95486NEWT:58002NEWT:9103NEWT:4577NEWT:1416333NEWT:5664NEWT:2157NEWT:418985NEWT:146479NEWT:10306NCBITaxon:2759NEWT:1911079NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:3635NEWT:5811NEWT:235443NEWT:1480154NEWT:1274414NEWT:27606NEWT:59202NEWT:9975NEWT:9612NEWT:38865NEWT:51953NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:169963NEWT:36329NEWT:1147787NCBITaxon:3044782NEWT:499175NEWT:72407NEWT:476272NEWT:349741NEWT:9606NEWT:367830NEWT:157295NEWT:641501NEWT:178616NEWT:410289NEWT:373153NEWT:7668NEWT:915099NEWT:74940NEWT:9721NEWT:1450511NEWT:360094NEWT:470NEWT:411901NEWT:1313NEWT:411469NEWT:84023NEWT:9838NEWT:105884NCBITaxon:9615NCBITaxon:5811NEWT:58334NEWT:411464NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:411460NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:411470NEWT:33952NEWT:2094720NCBITaxon:2697049NEWT:1274432NEWT:1274426NEWT:1423NEWT:4932NEWT:70448NEWT:9825NEWT:1274423NEWT:3603NEWT:393765NEWT:698936NEWT:2759NEWT:3847NEWT:39946NEWT:9823NEWT:178876NEWT:9940NEWT:327160NEWT:573NEWT:521001NEWT:39947NEWT:9031NEWT:1274420NEWT:7091NEWT:5784580000-0001-6950-4328