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Mylonas"],"technology_type":["Data-dependent acquisition","Mass Spectrometry"],"software":[""],"submitter_keywords":["Temporal","Phosphoproteome","Platelets","Procoagulant","Coat"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD062271"],"tissue":["Blood Platelet","Platelet"],"sample_protocol":["Platelets in  2% SDS, 10.3 mM DTT, 10.7 mM EDTA and 1X PhosStop, were thawed rapidly and heated at 95°C for 10 min. Protein concentration was determined using the tryptophane fluorescence method. Trypsin digestion of 120 µg of protein material per sample was carried out according to the SP3 method as described (using the magnetic Sera-Mag Speedbeads (50 mg/mL). Briefly, after heating at 95°C to denature and reduce disulfides, cysteines were alkylated by reaction with 32 mM iodoacetamide (final concentration) for 1 h in the dark at RT. Beads were added at a ratio 10:1 (w:w) to samples, and proteins were precipitated on beads with 60% ethanol (final concentration). After 3 washes with 80% ethanol, beads were digested in 45ul of 50 mM HEPES pH 8.3 with 3.0 µg of trypsin. After 1h of incubation at 37°C, the same amount of trypsin was added to the samples for an additional 1h of incubation. Supernatant after digestion were recovered, transferred to new tubes and used directly for tandem mass tag (TMT) labelling. Peptide mixtures in 45 µl of 50 mM HEPES pH 8.3 were mixed with 0.4 mg of TMT 10-plex reagents dissolved in 22 µl of pure acetonitrile (ACN) and reacted for 1h at RT. The reaction was quenched by adding 7 µl of 5% (v/w) hydroxylamine and incubating for 15min at RT. Individual labelling of samples was verified to be >98% by LC-MS analysis on a 60 min analysis. TMT labelled samples were pooled, the mixture obtained was acidified with 0.8% formic acid (final conc. v/v), frozen and the volume reduced by 90% by evaporation. After adding 9 volumes of aqueous 0.1% trifluoroacetic acid and centrifugation, peptides were desalted on a C18 SepPak 1cc 50mg cartridge. An aliquot of 10% of the eluate was dried and analyzed by MS as described below to assess labelling efficiency (which was found to be higher than 98.5%) and to derive total protein ratios for normalization. The remaining of the TMT mix was dried, redissolved, and processed for phosphopeptide enrichment by IMAC using the High-Select™ Fe-NTA Phosphopeptide Enrichment according to instructions from the manufacturer. The eluate from the IMAC column was dried and resuspended in 70 µl of 2% ACN, 0.05% TFA for LC-MS/MS analysis. Tryptic peptide mixtures were injected on an Ultimate RSLC 3000 nanoHPLC system interfaced to an Orbitrap Fusion Tribrid mass spectrometer. Peptides were loaded onto a trapping microcolumn Acclaim PepMap100 C18 (20 mm x 100 μm ID, 5 μm, 100 Å) before separation on a reverse-phase custom packed nanocolumn (75 μm ID × 40 cm, 1.8 μm particles). A flowrate of 0.25 μl/min was used with a gradient from 4 to 76% ACN in 0.1% formic acid (total method time: 140 min). Both total proteome and phospho-enriched samples were injected multiple times with different methods and either with a normal nanospray ion source or a Field Asymmetric Waveform Ion Mobility Spectrometry interface.  For analyses with the normal nanoLC interface, a data-dependent acquisition method controlled by Xcalibur 4.2 software (Thermo Fisher Scientific) was used that optimized the number of precursors selected (“top speed”) of charge 2+ to 5+ while maintaining a fixed scan cycle of 1.5 s. The precursor isolation window used was 0.7 Th. Peptides were fragmented by higher energy collision dissociation (HCD) with a normalized energy of 37% or 40% using two separate methods (two serial injections). MS2 scans were done at a resolution of 50’000 in the Orbitrap cell, to resolve 10-plex TMT reporter ions. The m/z of fragmented precursors was then dynamically excluded from selection during 120 s.  For analyses with the FAIMSpro interface, data-dependent acquisition methods controlled by Xcalibur 4.2 software were used, that alternated between two compensation voltages (CV) to acquire two survey scans within each cycle. Three methods were used, with the following CV pairs: -40/-60V, -50/-70V, -45/-55V. Following each survey scan at each CV, a “top speed” acquisition was performed to accumulate a maximum of MS2 spectra while keeping a maximum total cycle time of 1.8 s. MS2 scans were acquired with a normalized collision energy of 37%. All other parameters for MS2 spectra acquisition were the same as for the methods without FAIMS separation. Dynamic exclusion was performed to consider presence of different charge states for the same precursor in adjacent scans with different CVs."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Raw MS files obtained with FAIMS ion separation were split into independent files relative to each CV using the software Freestyle 1.6.90.0. All tandem MS data were processed by the MaxQuant software (version 1.6.14.0) incorporating the Andromeda search engine. The UNIPROT-SWISSPROT human proteome database of September 2020 was used (20’371 sequences), supplemented with sequences of common contaminants. Trypsin (cleavage at K, R) was used as the enzyme definition, allowing 2 missed cleavages. Carbamidomethylation of cysteine was specified as a fixed modification. N-terminal acetylation of protein, oxidation of methionine and phosphorylation on Ser, Thr and Tyr were specified as variable modifications. All identifications were filtered at 1% FDR at both the peptide and protein levels with default MaxQuant parameters. The isobaric match between runs functions of MaxQuant was used. For comparison of TMT runs, ratios were automatically calculated by MaxQuant as a function of the reference channel (baseline sample of each TMT).  MaxQuant data were further processed with Perseus software for the filtering step. For the phosphoproteomic data, only the phosphosites for which an intensity was quantified in all channel/sample were kept unless otherwise stated. Log2-transformation of the data were performed. The median normalization across the samples of a TMT was performed to account for differences in total loaded material. For the proteome analysis only, single peptide data were removed."],"omics_type":["Proteomics"],"labhead":["Lorenzo Alberio"],"instrument_platform":[""],"labhead_affiliation":["Division of Hematology and Central Hematology Laboratory, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["42598628 Veuthey L, Quadroni M, Jan M, Bertaggia Calderara D, Pereira Portela C, Gautier LA, Shehwar D, Aliotta A, Alberio L. Temporal phosphoproteomics reveals key regulators of procoagulant COAT platelet generation. Blood Vessel Thromb Hemost. 2026 3(3):100181 10.1016/j.bvth.2026.100181"],"submitter_mail":["roman.mylonas@unil.ch"],"submitter_affiliation":["Protein Analysis Facility, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland"],"submitter_country":["Switzerland"],"pubmed_abstract":["Procoagulant platelets play a major role in stabilizing the primary hemostatic plug formed by aggregated platelets. The intracellular signaling pathways driving the shift from an aggregatory to a procoagulant COAT platelet phenotype upon collagen plus thrombin stimulation are only partially elucidated. Aiming at identifying differentially phosphorylated proteins and potential regulators of the procoagulant response, we mapped time-dependent changes in the phosphoproteome of aggregatory vs procoagulant COAT platelets using a liquid chromatography-mass spectrometry-based temporal phosphoproteomics approach. Upon stimulation with convulxin (an agonist of the collagen receptor glycoprotein VI) and thrombin, we observed that all platelets rapidly increased their overall phosphorylation during the first minute. Afterward, aggregatory platelets maintained or further increased their phosphorylation levels, whereas procoagulant COAT platelets exhibited a progressive and marked decrease in phosphorylation. Notably, during the first minute after activation, before the phenotypic development of the procoagulant response, several ion channels (calcium, sodium, hydrogen, and chloride), proteins involved in receptor negative feedback loops, cyclic nucleotide-dependent regulatory proteins, GTPases, and key kinases were already differentially phosphorylated in procoagulant COAT vs aggregatory experimental conditions. At the onset of the procoagulant response (1-3 minutes after activation), some calcium channels, phosphatidylinositol transfer proteins, α2-adrenergic receptors, and proteins involved in intracellular and extracellular mechanisms regulating integrin αIIbβ3 functionality were also differentially phosphorylated. This study highlights the usefulness of assessing phosphorylation dynamics to identify very early phosphorylation events and to understand the rapid phenotypic switch from aggregatory to procoagulant COAT platelets. This approach identified several candidate proteins and mechanisms likely to initiate and modulate the procoagulant response."],"pubmed_title":["Temporal phosphoproteomics reveals key regulators of procoagulant COAT platelet generation."],"pubmed_authors":["Veuthey Lucas L, Quadroni Manfredo M, Jan Maxime M, Bertaggia Calderara Debora D, Pereira Portela Cindy C, Gautier Lucas A LA, Shehwar Durre D, Aliotta Alessandro A, Alberio Lorenzo L"],"additional_accession":[]},"is_claimable":false,"name":"Temporal phosphoproteomics reveals key regulators of procoagulant COAT platelet generation","description":"The intracellular signaling generating and sustaining the procoagulant response of platelets from a common aggregatory phenotype upon simultaneous collagen and thrombin (COAT) stimulation is only partially elucidated. Here we described the phosphoproteome of aggregatory and procoagulant COAT platelets using a temporal phosphoproteomic approach (tandem-mass-tag labelling and liquid-chromatography mass-spectrometry) to reveal differentially regulated proteins and pathways and possibly regulators of the procoagulant response. Upon stimulation, all platelets acquire an overall increased phosphorylation status up to one minute. Then, as procoagulant COAT platelets are generated from aggregatory ones, the global phosphorylation status is maintained in aggregatory platelets whereas it is gradually and strongly decreased in procoagulant COAT platelets over time. Prior the procoagulant response (0-1min post-activation), calcium/sodium/hydrogen/chloride channels, glycoprotein VI-dependent negative feedback loops, cyclic nucleotide-dependent inhibitory pathways, and cytoskeleton interactors were already differentially phosphorylated in COAT versus AGG conditions. At the onset of the procoagulant response (1-3min post-activation), calcium channels, phosphatidylinositol-transfer proteins, thromboxane and α2-adrenergic receptors were differentially phosphorylated. When both platelet phenotypes were stable (8min), numerous cytoskeleton proteins were decreased and signaling proteins were importantly dephosphorylated. Moreover, adhesive proteins, small GTPases, cytoskeleton-related proteins, and calcium-regulating proteins were differentially phosphorylated. This study therefore proposes several relevant targets for modulating the procoagulant response and highlights the relevance of studying time-resolved phosphorylation events in the frame of the rapid phenotypic switch from aggregatory to procoagulant platelet.","dates":{"publication":"2026-09-14","submission":"2025-03-26"},"accession":"PXD062271","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:108018","NEWT:377960","NEWT:1131","NEWT:35795","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NEWT:1334565","NEWT:625351","NEWT:258594","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:57577","NEWT:247480","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:2315688","NEWT:592321","NEWT:1073882","NEWT:6819","NEWT:77173","NEWT:112509","NEWT:46429","NEWT:475174","NEWT:111205","NEWT:1599","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:32264","NEWT:12215","NEWT:1590","NEWT:10034","NEWT:33114","NEWT:1596","NEWT:2736291","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:294671","NEWT:376619","NEWT:1748418","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:3767","NEWT:1589","NEWT:1907535","NEWT:135622","NEWT:4615","NEWT:67352","NEWT:672127","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656061","NEWT:37965","NEWT:656064","NEWT:1582","NEWT:3760","NEWT:1584","NEWT:2086595","NEWT:36630","NEWT:1585","NEWT:383379","NEWT:381198","NEWT:418106","NCBITaxon:12721","NEWT:166340","NEWT:10029","NEWT:913645","NEWT:2492962","NEWT:641809","NEWT:44250","NEWT:1392488","NEWT:38815","NEWT:317447","NEWT:5537","NEWT:4688","NEWT:3357","NEWT:111225","NEWT:7719","NEWT:29073","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:1562698","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:29064","NEWT:2767846","NEWT:108061","NEWT:60711","NEWT:2020713","NEWT:224308","NEWT:273791","NEWT:3347","NEWT:49928","NEWT:3349","NEWT:160621","NEWT:2502409","NEWT:212790","NEWT:110368","NEWT:55350","NEWT:1916073","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:468822","NEWT:1912919","NEWT:410658","NEWT:5516","NEWT:44688","NEWT:44689","NEWT:370038","NEWT:498211","NEWT:345076","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:33554","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:1310173","NEWT:200795","NEWT:37919","NEWT:342808","NEWT:2579791","NEWT:171719","NEWT:44685","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:260499","NEWT:410661","NEWT:329854","NEWT:1140","NCBITaxon:2157","NEWT:2066563","NEWT:2649329","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:150808","NEWT:709964","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:156974","NEWT:3714","NCBITaxon:37162","NEWT:270643","NEWT:3715","NEWT:1538","NEWT:2065263","NEWT:199225","NEWT:177437","NEWT:717966","NEWT:9014","NEWT:10891","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:29022","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:66440","NEWT:1245466","NEWT:3704","NEWT:244366","NEWT:1246791","NEWT:176597","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:9006","NEWT:33548","NEWT:52299","NEWT:1883426","NEWT:8165","NEWT:96794","NEWT:34878","NEWT:10401","NEWT:10886","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:926571","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:1955249","NEWT:215451","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:2714896","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:1608994","NEWT:33995","NEWT:55784","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:329032","NEWT:56636","NEWT:2709072","NEWT:2499525","NEWT:55307","NEWT:1122981","NEWT:2853422","NEWT:1122984","NEWT:487","NEWT:1538553","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:45972","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:2836","NEWT:376686","NEWT:237610","NEWT:95486","EFO:0001352","NEWT:1385720","NEWT:219809","NEWT:219808","NEWT:119562","NEWT:1883446","NEWT:31345","NEWT:1233435","NEWT:118223","NEWT:11757","NEWT:141469","NEWT:987059","NEWT:109760","NEWT:29031","NEWT:1945864","NEWT:317047","NEWT:1509","NEWT:491","NEWT:460523","NEWT:45954","NEWT:1578","NEWT:235443","NEWT:1579","NEWT:133894","NEWT:1757312","NEWT:85694","NEWT:109786","NEWT:1922344","NEWT:108458","NEWT:5936","NEWT:85692","NEWT:321967","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:279010","NEWT:291146","NEWT:29466","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:415978","NEWT:235455","NEWT:1255228","NEWT:410289","NEWT:191701","NEWT:373153","NEWT:1640278","NEWT:9054","NEWT:472","NEWT:940825","NEWT:29459","NEWT:529507","NEWT:1071661","NEWT:1380096","NEWT:28128","NEWT:470","NEWT:41122","NEWT:5911","NEWT:1328300","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:911022","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:717989","NEWT:33952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