{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075498/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075498/2025MZ018_CRIS_001_01_4_5ug_DIA.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075498/2025MZ018_CRIS_003_01_4_5ug_DDA.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075498/2025MZ018_CRIS_002_01_4_5ug_DIA.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075498/2025MZ018_CRIS_001_01_4_5ug_DDA.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075498/2025MZ018_CRIS_002_01_4_5ug_DDA.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075498/2025MZ018_CRIS_003_01_4_5ug_DIA.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075498/2025MZ018_CRIS_001_01_4_5ug_DDA.pdResult","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075498/2025MZ018_CRIS_002_01_4_5ug_DDA.pdResult","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075498/2025MZ018_CRIS_003_01_4_5ug_DDA.pdResult"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"labhead_mail":["eduard.sabido@crg.eu"],"submitter":["Cristina Chiva"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Dda","Histones","Marks","Dia"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD075498"],"sample_protocol":["10 µg of histones from calf thymus (Roche #10223565001) were derivatized in triplicates with propionic anhydride, digested with trypsin and derivatized again with phenyl isocyanate . Briefly, samples were dissolved in 9 µL of H2O and 1 µL of HEPES 0.5M was added to bring the pH to 8.5. The propionic anhydride was prepared by adding 1 µL of propionic anhydride to 99 µL of H2O, and 1 µL of propionic anhydride solution was immediately added to the samples with vortexing and incubation for 2 minutes. The reaction was quenched with 1 µL of 80 mM hydroxylamine and samples were incubated at room temperature for 20 minutes. Tryptic digestion was performed for 3 h with 0.1 μg trypsin at 37 ºC (Promega cat # V5113) per sample. A fresh solution of phenyl isocyanate was prepared by adding 1 µL of phenyl isocyanate to 99 µL of ACN and 3 µL of phenyl isocyanate solution was immediately added to the samples with vortexing and incubation for 60 minutes. Samples were acidified by adding 50 µL of 5% formic acid, vacuum dried and desalted with C18 ultramicrospin columns (The Nest Group, Inc, Southborough, USA).A 5 μg aliquot of the peptide mixture were analyzed using a LTQ-Orbitrap Eclipse mass spectrometer (Thermo Fisher Scientific, San Jose, USA) coupled to an EASY-nLC 1200 (Thermo Fisher Scientific, San Jose, USA) in both data independent acquisition (DIA) and data dependent acquisition (DDA) methods.Peptides were loaded directly onto the analytical column and were separated by reversed-phase chromatography using a 50-cm column with an inner diameter of 75 μm, packed with 2 μm C18 particles spectrometer (Thermo Scientific, San Jose, USA) with a 60 min chromatographic. The mass spectrometer was operated in positive ionization mode on both DDA and DIA modes. The DDA method was driven by the “Top Speed” acquisition algorithm, which determined the number of selected precursor ions for fragmentation, whilst the DIA method consisted in repetitive acquisition cycles of 25 staggered windows of 24 m/z covering a mass range from 350 to 1850 m/z."],"repository":["Pride"],"quantification_method":["Not available"],"modification":["","N6"],"data_protocol":["Data dependent acquisition runs were analyzed using the Proteome Discoverer software suite (v 2.5, Thermo Fisher Scientific), and the Mascot  search engine (v2.6, Matrix Science) was used for peptide identification. Data were searched against the SwissProt Bovine database plus the most common contaminants. A first search was done considering propionylation on lysines and phenyl isocyanate on N-terminal as variable modifications. With the proteins obtained in this search, a new database was generated, and a second database search was done considering propionylation on protein N-terminal and phenyl isocyante on N-terminal as fixed modification and propionylation on lysines, dimethyl lysine, trimethyl lysine, propionyl + methyl lysine, and acetyl lysine as variable modifications. Precursor ion mass tolerance of 7 ppm at the MS1 level was used, and up to 5 missed cleavages for trypsin were allowed. False discovery rate (FDR) in peptide identification was set to a maximum of 5% and a threshold of MASCOT ion score od 20 was applied. The results from the Proteome Discoverer software were used to generate a library in the Skyline  software (v 25.1.1.174) that was used to detect, extract and quantify the MS1 and MS2 signal of the histone peptides and their variants from the DIA runs."],"omics_type":["Proteomics"],"labhead":["Eduard Sabidó"],"instrument_platform":[""],"labhead_affiliation":["1Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain. 2Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain."],"submission_type":["PARTIAL"],"species":["Bos Taurus (bovine)"],"publication":["42253128 Nameni A, Declercq A, Gabriels R, Devreese R, Degroeve S, De Maesschalck A, Dhaenens M, Chiva C, Sabidó E, Martens L, Bouwmeester R. iDeepLC: Chemical Structure Information Yields Improved Retention Time Prediction of Peptides with Unseen Modifications. Anal Chem. 2026 10.1021/acs.analchem.5c08017"],"submitter_mail":["cristina.chiva@upf.edu"],"submitter_affiliation":["University Pompeu Fabra"],"submitter_country":["Spain"],"pubmed_abstract":["Deep learning has notably advanced the field of liquid chromatography-mass spectrometry-based proteomics. Accurate prediction of peptide retention times significantly enhances our ability to match LC-MS data with the correct peptides and proteins, especially for data-independent acquisition data. While numerous models predict peptide LC retention times with high accuracy, few can accurately predict the retention times of chemically modified peptides, particularly those with modifications not encountered during model training. In our previously developed DeepLC model, accurate predictions could be made for unseen modifications by leveraging the chemical compositions of (modified) residues. Here, however, we present a further enhancement of this model based on the chemical structural information. The resulting model, called iDeepLC, shows overall more accurate predictions and better generalization performance for predicting the retention time of modifications structurally defined as SMILES but unseen during training than DeepLC. iDeepLC is freely available as an open-source software under the Apache2 license and can be found at https://github.com/CompOmics/iDeepLC."],"pubmed_title":["iDeepLC: Chemical Structure Information Yields Improved Retention Time Prediction of Peptides with Unseen Modifications."],"pubmed_authors":["Nameni Alireza A, Declercq Arthur A, Gabriels Ralf R, Devreese Robbe R, Degroeve Sven S, De Maesschalck Amélie A, Dhaenens Maarten M, Chiva Cristina C, Sabidó Eduard E, Martens Lennart L, Bouwmeester Robbin R"],"additional_accession":[]},"is_claimable":false,"name":"DDA and DIA analysis of calf thymus histone modifications using Prop-PIC derivatization","description":"Comprehensive analysis of rhe histone marks from calf thymus","dates":{"publication":"2026-06-15","submission":"2026-03-11"},"accession":"PXD075498","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:3555","NEWT:241368","NEWT:2","NEWT:157546","NEWT:190802","NEWT:35554","NEWT:9778","NEWT:150475","NEWT:9417","NEWT:347515","NEWT:1216979","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:5180","NEWT:256737","NEWT:2042546","NEWT:115104","NEWT:1081927","NEWT:67825","NEWT:185579","NEWT:43179","NEWT:13076","NEWT:1249668","NEWT:317","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:415540","NEWT:876138","NEWT:4081","NEWT:554","NEWT:98334","NEWT:426428","NEWT:237561","NEWT:6928","NEWT:10036","NEWT:7574","NEWT:1351","NEWT:7215","NEWT:29204","NEWT:272563","NEWT:507601","NCBITaxon:79857","NCBITaxon:6157","NEWT:95648","NEWT:3885","NEWT:746360","NEWT:6239","NEWT:3888","NEWT:1589","NEWT:470150","NEWT:135622","NEWT:216257","NEWT:6915","NEWT:9986","NEWT:101510","NEWT:4054","NEWT:3880","NEWT:3641","NEWT:383379","NEWT:8782","NEWT:1263854","NEWT:1000589","NEWT:1902","NEWT:85962","NEWT:160488","NEWT:28104","NEWT:317447","NEWT:7955","NCBITaxon:2","NEWT:985076","NEWT:7959","NEWT:2261","NEWT:4565","NEWT:1264690","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:216595","NEWT:243230","NEWT:8355","NEWT:1283","NEWT:931281","NEWT:1000561","NEWT:7029","NEWT:1283300","NEWT:6183","NEWT:6063","NEWT:334747","NEWT:61235","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:436486","NEWT:6287","NEWT:2242","NEWT:300641","NEWT:4784","NEWT:727","NEWT:9796","NEWT:725","NEWT:360106","NEWT:260707","NEWT:287","NEWT:10117","NEWT:10239","NCBITaxon:6191","NEWT:10116","NEWT:1280","NEWT:1836","NEWT:1735272","NEWT:83334","NEWT:185431","NEWT:83332","NEWT:29760","NEWT:260704","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:44685","NEWT:2697049","NEWT:1148","NEWT:11676","NEWT:55571","NEWT:100226","NCBITaxon:6073","NEWT:4530","NEWT:4896","NEWT:6279","NEWT:1123869","NEWT:7370","NEWT:75058","NEWT:83906","NEWT:607699","NEWT:6282","NEWT:1094343","NEWT:208964","NEWT:1134506","NEWT:575584","NEWT:296543","NEWT:1773","NEWT:38783","NEWT:8727","NEWT:1895","NEWT:1182590","NEWT:8726","NEWT:6669","NEWT:10090","NEWT:935293","NEWT:64152","NEWT:749200","NEWT:4120","NEWT:51515","NEWT:5693","NEWT:8724","NEWT:51511","NEWT:92867","NEWT:8723","NEWT:990346","NEWT:5334","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:230741","NEWT:284812","NCBITaxon:10359","NCBITaxon:1313","NEWT:43330","NEWT:242619","NEWT:44544","NEWT:632957","NEWT:373995","NEWT:5689","NEWT:645463","NEWT:544404","NEWT:3702","NEWT:129249","NEWT:9925","NEWT:8839","NEWT:4232","NEWT:990119","NEWT:2758385","NEWT:4113","NEWT:837","NEWT:11298","NEWT:171101","NEWT:421932","NEWT:196627","NEWT:408172","NEWT:5691","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:627025","NEWT:400772","NEWT:1097677","NEWT:3708","NEWT:128161","NEWT:106592","NEWT:1117957","NEWT:9913","NEWT:1432138","NEWT:10312","NEWT:1424507","NEWT:4100","NEWT:1076","NEWT:6763","NEWT:803","NEWT:8030","NEWT:29722","NEWT:380394","NEWT:1692259","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:180066","NEWT:67767","NEWT:46835","NEWT:135588","NEWT:1843183","NEWT:95486","NEWT:58002","NEWT:9103","NEWT:4577","NEWT:1416333","NEWT:5664","NEWT:2157","NEWT:146479","NEWT:10306","NCBITaxon:2759","NEWT:1911079","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:1480154","NEWT:1274414","NEWT:27606","NEWT:59202","NEWT:9975","NEWT:3197","NEWT:9615","NEWT:10299","NEWT:860688","NEWT:884019","NEWT:169963","NEWT:36329","NEWT:1147787","NCBITaxon:3044782","NEWT:72407","NEWT:9606","NEWT:367830","NEWT:157295","NEWT:641501","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:915099","NEWT:74940","NEWT:1450511","NEWT:360094","NEWT:470","NEWT:84023","NEWT:9838","NCBITaxon:9615","NEWT:58334","NEWT:1193501","NEWT:3055","NEWT:6326","NEWT:6689","NEWT:2762","NEWT:5476","NEWT:1174673","NEWT:562","NEWT:33952","NEWT:1274432","NEWT:1274426","NEWT:1423","NEWT:4932","NEWT:70448","NEWT:9825","NEWT:1274423","NEWT:3603","NEWT:698936","NEWT:2759","NEWT:3847","NEWT:39946","NEWT:9823","NEWT:178876","NEWT:9940","NEWT:327160","NEWT:573","NEWT:9031","NEWT:1274420","NEWT:7091","NEWT:578458"],"pubmed":["42253128"],"ORCID":["0000-0001-8150-6203"]}}