{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075694/sample_metadata.tsv"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075694/checksum.txt"],"Csv":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075694/Pro1_Report.csv"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075694/TimsTOFPro1_Entrapment_Trimmed.psar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075694/TimsTOFPro1_HCP_Assay1.psar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075694/TimsTOFPro_HCP_Assay4.psar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075694/TimsTOFPro_HCP_Assay3.psar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075694/TimsTOFPro1_HCP_Assay2.psar","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075694/Assay1_raw.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD075694/TimsTOFPro1_Entrapment_Shuffled.psar"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["somar.x.khalil@gsk.com"],"submitter":["Somar khalil"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"software":["Not available"],"submitter_keywords":["Host cell proteins","Biotherapeutics","Analytical validation","Lc–ms/ms","Ich q2(r2)","Hcp quantification","Untargeted proteomics","Timstof","Ddapasef"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD075694"],"sample_protocol":["Samples consisted of the NIST monoclonal antibody reference material (RM 8671) spiked with a stable isotope-labeled CHO whole-proteome standard (SILu™CHOP). Seven spike levels corresponding to 20–80 ng total HCP were prepared. Each sample contained 20 µg of NISTmAb and the appropriate SIL-HCP spike amount. Samples were denatured in 0.125% RapiGest in 50 mM TEAB, reduced with dithiothreitol at 50 °C for 40 min, and alkylated with iodoacetamide for 25 min in the dark. Proteolytic digestion was performed overnight (~14 h) at 37 °C using a Trypsin/Lys-C mixture at a 1:40 enzyme-to-substrate ratio. Digestion was quenched with trifluoroacetic acid and acid-labile surfactant was hydrolyzed at 37 °C. Peptides were desalted using C18 spin columns, dried, and reconstituted prior to LC-MS/MS analysis. Approximately 500 ng of peptides were loaded onto Evotip C18 cartridges for nanoLC separation."],"repository":["pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Raw data were processed using SpectroMine v5.2 with fixed search parameters applied across all assays. Database searching used the Cricetulus griseus UniProt reference proteome supplemented with NISTmAb sequences and MassPREP digestion standards. Trypsin/P specificity was specified with up to one missed cleavage. Carbamidomethylation of cysteine and stable isotope labeling of lysine and arginine were defined as fixed modifications. Peptides were restricted to 7–30 amino acids with charge states 2+–3+. Target–decoy competition was used for q-value estimation and peptide-spectrum matches, peptides, and protein groups were filtered at q ≤ 0.01. Quantification was performed from MS1 precursor intensities using a Hi3-based approach. Downstream statistical analysis and validation modeling were conducted in Python with deterministic protein inference and hierarchical variance modeling."],"omics_type":["Proteomics"],"labhead":["Somar Khalil"],"instrument_platform":[""],"labhead_affiliation":["Technical Research & Development, GSK"],"submission_type":["PARTIAL"],"species":["Mus Musculus (mouse)"],"submitter_mail":["somar.x.khalil@gsk.com"],"publication":["42201109 Khalil S, Dierick JF, Bourguignon P, Plisnier M. Prospective ICH Q2(R2)-Aligned Total-Error Validation of Label-Free Untargeted Proteomics for Host Cell Protein Quantification in Biotherapeutics. Proteomes. 2026 14(2):21 10.3390/proteomes14020021"],"submitter_affiliation":["GSK"],"submitter_country":["Belgium"],"additional_accession":[]},"is_claimable":false,"name":"Prospective ICH Q2(R2)-aligned validation of label-free untargeted proteomics for host cell protein quantification in biotherapeutics","description":"This dataset contains raw and processed LC–MS/MS data generated for a prospective validation of label-free untargeted proteomics for host cell protein (HCP) quantification in biotherapeutic matrices. A stable isotope-labeled CHO whole-proteome standard was spiked into the NIST monoclonal antibody reference material (RM 8671) across seven concentration levels (20–80 ng total HCP per injection). Samples were analyzed using an Evosep One nanoLC system coupled to a Bruker timsTOF Pro operating in ddaPASEF mode. The study comprised four independent analytical assays totaling 198 injections and was designed to evaluate analytical performance characteristics under an ICH Q2(R2) total-error validation framework. The dataset supports evaluation of identification error control, quantitative trueness, precision, intermediate precision, and total error across the validated range. Raw Bruker timsTOF acquisition files and identification results generated with SpectroMine are provided together with the FASTA database and analysis parameters to ensure full reproducibility.","dates":{"publication":"2026-06-08","submission":"2026-03-16"},"accession":"PXD075694","cross_references":{"TAXONOMY":["NEWT:1773","NEWT:6945","NEWT:3555","NEWT:38783","NEWT:8727","NEWT:1182590","NEWT:8726","NEWT:2","NEWT:157546","NEWT:10090","NEWT:935293","NEWT:749200","NEWT:35554","NEWT:4120","NEWT:5693","NEWT:9417","NEWT:347515","NEWT:8724","NEWT:1216979","NEWT:307972","NEWT:92867","NEWT:8723","NEWT:990346","NEWT:544496","NEWT:5334","NEWT:145953","NEWT:257309","NEWT:5180","NEWT:284812","NEWT:115104","NCBITaxon:1313","NEWT:1081927","NEWT:43330","NEWT:67825","NEWT:44544","NEWT:13076","NEWT:1249668","NEWT:373995","NEWT:544404","NEWT:3702","NEWT:8839","NEWT:317","NEWT:4232","NEWT:990119","NEWT:1736309","NEWT:4113","NEWT:7227","NEWT:11298","NEWT:7469","NEWT:885318","NEWT:171101","NEWT:876138","NEWT:4081","NEWT:554","NEWT:5691","NEWT:98334","NEWT:408170","NEWT:260710","NEWT:627025","NEWT:3708","NEWT:106592","NEWT:237561","NEWT:9913","NEWT:10036","NEWT:4100","NEWT:7574","NEWT:1351","NEWT:1076","NEWT:6763","NEWT:7215","NEWT:803","NEWT:8030","NEWT:380394","NEWT:272563","NEWT:507601","NEWT:1639","NEWT:188229","NEWT:4909","NCBITaxon:79857","NEWT:95648","NEWT:746360","NEWT:6239","NEWT:1589","NEWT:135588","NEWT:135622","NEWT:216257","NEWT:6915","NEWT:9986","NEWT:101510","NEWT:95486","NEWT:3880","NEWT:58002","NEWT:9103","NEWT:4577","NEWT:5664","NEWT:2157","NEWT:146479","NEWT:1911079","NEWT:1000589","NEWT:145943","NEWT:1902","NEWT:85962","NEWT:160488","NEWT:317447","NEWT:3635","NEWT:7955","NCBITaxon:2","NEWT:235443","NEWT:1480154","NEWT:985076","NEWT:7959","NEWT:2261","NEWT:3197","NEWT:9615","NEWT:884019","NEWT:4565","NEWT:1264690","NEWT:169963","NCBITaxon:38727","NEWT:36329","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:9606","NEWT:367830","NEWT:157295","NEWT:243230","NEWT:931281","NEWT:373153","NEWT:7029","NEWT:1283300","NEWT:334747","NEWT:470","NCBITaxon:79824","NCBITaxon:4563","NEWT:3218","NEWT:5759","NEWT:9838","NCBITaxon:9615","NEWT:1736231","NEWT:1193501","NEWT:3055","NEWT:6287","NEWT:2242","NEWT:6326","NEWT:9796","NEWT:2762","NEWT:5476","NEWT:1174673","NEWT:562","NEWT:260707","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1836","NEWT:1735272","NEWT:29760","NEWT:260705","NEWT:80863","NEWT:1148","NEWT:4932","NEWT:70448","NEWT:9825","NEWT:3603","NEWT:698936","NEWT:2759","NEWT:39946","NEWT:11676","NEWT:9823","NEWT:100226","NCBITaxon:6073","NEWT:4530","NEWT:4896","NEWT:6279","NEWT:7370","NEWT:573","NEWT:6282","NEWT:7091","NEWT:1134506"],"pubmed":["42201109"],"ORCID":["0000-0001-6263-8884"]}}