{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD074199/immunopeptidome_context_e_spectronaut.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD074199/immunopeptidome_context_abcd_spectronaut.tsv"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD074199/OE2-20230804_002_DIA.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD074199/OE2-20230203_017_DIA.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD074199/OE2-20230214_006_DIA.raw"],"Xls":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD074199/immunopeptidome_context_f_spectronaut.xls"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD074199/files_dia.md"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"labhead_mail":["anglika.riemer@dkfz.de"],"submitter":["Jonas Förster"],"technology_type":["Immunopeptidomics","Mass Spectrometry","Data-independent acquisition"],"software":[""],"submitter_keywords":["Immunopeptidomics","Targeted","Prm","Hpv","Cancer"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD074199"],"tissue":["Cell Culture"],"sample_protocol":["CaSki (RRID: CVCL_1100) cells were obtained from ATCC and were cultivated in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin and 2 mM L- glutamine. Goerke ()) cells were obtained from Andreas Kaufmann (Charité, Berlin, Germany) and were cultivated in Eagles’s MEM medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, 2 mM L-glutamine and 1% MEM NEAA. W12-20861 (Jeon & Lambert, 1995) cells were obtained from Paul Lambert, University of Wisconsin, Madison, WI, USA and were cultivated in Ham‘s F-12 medium supplemented with 25% DMEM, 5% fetal bovine serum, 1% penicillin/streptomycin, 0.4 mg/ml hydrocortisone, 0.5 μg/ml cholera toxin and 5 μg/ml insulin. Cells were kept under standard conditions in a humidified incubator at 37 °C and 5% CO2. For the immunoprecipitation of HLA:peptide complexes, cells were washed with ice-cold PBS and harvested using Accutase (Thermo Fisher Scientific, Waltham, MA, USA). Dry cell pellets were snap frozen in liquid nitrogen and stored at −20 °C until further usage. Cell lines were regularly authenticated and confirmed to be free of Mycoplasma, SMRV, or interspecies contamination by SNP profiling and multiplex-PCR by Multiplexion GmbH (Schmitt & Pawlita, 2009). HLA class I peptide complexes were isolated from cell pellets using a 96-well plate-based immunoprecipitation (IP) protocol based on previously published protocols (Chong 2018, Bassani-Sternberg 2016). Cell pellets were lysed in IP lysis buffer (0.25% sodium deoxycholate, 1% n-octyl-β-D-glucopyranoside (OGP), 1 mM PMSF, 1 mM EDTA, 0.2 mM iodoacetamide (IAA), 1x cOmplete Mini Protease Inhibitor Cocktail in PBS) for 1 hour at 4°C. Lysates were cleared by centrifugation at 40,000 × g for 30 min at 4°C. The IP was performed on a 96-well filter plate (Agilent) using a Waters Positive Pressure-96 Processor. Each well was loaded with 150 µl of W6/32 antibody-crosslinked Protein A Sepharose bead suspension. Cleared lysate (equivalent of up to 50 × 10⁶ cells per well) was loaded by gravity flow. Beads were subsequently washed 8× with 1 ml IP wash buffer A (150 mM NaCl, 20 mM Tris-HCl, pH 8), 8× 1 ml IP wash buffer B (400 mM NaCl, 20 mM Tris-HCl, pH 8), 8× 1 ml IP wash buffer A, and 8× 1 ml IP wash buffer C (20 mM Tris-HCl, pH 8). Peptides were eluted with 2× 500 μl 0.3% trifluoroacetic acid (TFA). The eluate was reduced with 50 mM TCEP for 10 min, followed by alkylation with 400 mM IAA in the dark for 20 min. The peptides were desalted and purified using a Sep-Pak tC18 96-well plate (Waters). After sample loading, oxidation was performed by applying a freshly prepared 1:200 dilution of performic acid (5 μl of 30 % H2O2 and 45 μl of 10 % formic acid). Peptides were eluted with 28% acetonitrile (ACN) / 0.1% TFA, dried in a vacuum concentrator, and stored at -20°C. All analyses were performed on an UltiMate 3000 HPLC system coupled to an Orbitrap Exploris 480 mass spectrometer (Thermo Fisher Scientific) via a Nanospray Flex ion source. Peptides were separated on a nanoEase M/Z Peptide BEH C18 column (130 Å, 1.7 µm, 75 µm x 200 mm, Waters) at a flow rate of 300 nl/min using gradients from 0% to 80% solvent B (ACN, 0.1% FA) over up to 110 minutes. Dried peptide samples were resolubilized in 5% ACN / 0.1% TFA. For dynamic retention time (RT) alignment, samples were spiked with 50 fmol of Pierce Peptide Retention Time Calibration Mixture (PRTC, Thermo Fisher Scientific) and 5 fmol of a commercial retention time standardization kit (PROCAL, JPT Peptide Technologies, Zolg et al. 2017) per injection. Electrospray ionization was driven with an applied potential of 2500 V. A pulled emitter (CoAnn Technologies) with 20 μm inner diameter (ID) to 10 μm ID at the tip was used. Across all runs, the RF Lens was set to 50%, Automatic Gain Control (AGC) was enabled, lock mass was the polydimethylcyclosiloxane ion ([(Si(CH3)2O)6+H]+,445.120025 m/z) from ambient air in timed mode for the first 3 min. For global immunopeptidome analysis, a data-independent acquisition (DIA) method was used. The method consisted of one full MS1 scan (120,000 resolution, 300-1650 m/z, 300% AGC, 35 ms max. IT). This was followed by 44 consecutive MS2 scans using dynamic precursor isolation windows covering the 299.5-1650.5 m/z range with 1 m/z overlaps. MS2 spectra were acquired at 30,000 resolution with 30% NCE, a 3000% AGC target, and an automatic max. IT."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Untargeted DIA data were analyzed using Spectronaut (v. 17.6, Biognosys) with directDIA against a human and HPV16 protein database. Identifications were filtered to 1% PSM and 1% peptide FDR. For all detections, binding predictions for the respective HLA class I alleles of the sample were generated with netMHCpan (v. 4.1b, Reynisson et al., 2021). Data from direct infusion experiments were analyzed using custom R scripts to determine the optimal NCE that maximized the signal of the 4th-6th most intense fragment ions, ensuring at least six transitions were detectable. The R scripts are published on GitHub at https://github.com/jonasfoe/ms_targeted_workflows."],"omics_type":["Proteomics"],"labhead":["Angelika B. Riemer"],"instrument_platform":[""],"labhead_affiliation":["German Cancer Reseach Center (DKFZ)"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["42551630 Förster JD, Becker JP, Vučković N, Riemer AB. Systematic Workflow Optimization for Ultra-sensitive Targeted Immunopeptidomics. Mol Cell Proteomics. 2026 25(9):101634 10.1016/j.mcpro.2026.101634"],"submitter_mail":["jonasfoerster@gmail.com"],"submitter_affiliation":["German Cancer Reseach Center (DKFZ)"],"submitter_country":["Germany"],"pubmed_abstract":["Epitope detection sensitivity remains a primary bottleneck in mass spectrometry (MS)-based immunopeptidomics, as conventional discovery-based workflows such as data-dependent (DDA) and data-independent acquisition (DIA) frequently lack the sensitivity required to detect ultra-low abundant targets. While these untargeted methods are powerful for mapping the general immunopeptidome, the stochastic nature of precursor selection and the presence of complex, chimeric spectra mean that rare species, such as viral or mutation-derived neoepitopes, often remain undetected. In this study, we present optiPRM+, an ultra-sensitive targeted-first workflow for the Orbitrap Exploris 480 platform that integrates systematically optimized targeted acquisition with untargeted DIA contextualization to bridge this sensitivity gap. Our approach centers on the empirical characterization of target peptides using direct infusion-MS to determine optimal fragmentation conditions and inclusion list-driven data-dependent acquisition (iDDA). To maximize signal-to-noise ratios for these trace-level targets, we employed ultra-high MS2 resolutions (up to 480,000), ion injection times up to 1000 ms, and narrow precursor isolation windows. Additionally, we discovered that precursors with a charge state exceeding their basic amino acid count require unusually low energies for optimal fragmentation, which is especially relevant for the non-tryptic peptides characteristic of the immunopeptidome. We applied the optiPRM+ workflow to the challenging biological case of Human Papillomavirus type 16 (HPV16), a virus known to suppress antigen presentation pathways. This optimized strategy enabled the confident identification and validation of the human leukocyte antigen (HLA)-A∗02:01-restricted epitope TIHDIILECV and, to our knowledge, the first MS-based detection of two novel viral targets: ISEYRHYCY (HLA-A∗01:01) and CVYCKQQLLR (HLA-A∗11:01). Subsequent global immunopeptidome analysis via DIA confirmed that these ultra-low abundance peptides were not detectable through untargeted methods despite being clearly validated by our targeted approach. By successfully detecting these viral peptides, we demonstrate that a systematically optimized targeted-first approach can uncover biologically relevant epitopes that remain invisible to conventional discovery-based workflows."],"pubmed_title":["Systematic Workflow Optimization for Ultra-sensitive Targeted Immunopeptidomics."],"pubmed_authors":["Förster Jonas D JD, Becker Jonas P JP, Vučković Nika N, Riemer Angelika B AB"],"additional_accession":[]},"is_claimable":false,"name":"Systematic Workflow Optimization for Ultra-Sensitive Targeted Immunopeptidomics","description":"Epitope detection sensitivity remains a primary bottleneck in mass spectrometry (MS)-based immunopeptidomics, as conventional discovery-based workflows such as data-dependent (DDA) and data-independent acquisition (DIA) frequently lack the sensitivity required to detect ultra-low abundant targets. While these untargeted methods are powerful for mapping the general immunopeptidome, the stochastic nature of precursor selection and the presence of complex, chimeric spectra mean that rare species, such as viral or mutation-derived neoepitopes, often remain undetected. In this study, we present optiPRM+, an ultra-sensitive targeted proteomics workflow optimized for the Orbitrap Exploris 480 platform designed to bridge this sensitivity gap through systematic, peptide-specific parameter tuning. Our approach centers on the empirical characterization of target peptides using inclusion list-driven data-dependent acquisition (iDDA) and direct infusion-MS to determine optimal fragmentation conditions. We demonstrate that substantial sensitivity gains are achieved by pushing Orbitrap scanning parameters to their practical limits, specifically utilizing ultra-high MS2 resolutions of up to 480,000, maximum ion injection times of 1000 ms, and narrow precursor isolation windows to maximize signal-to-noise ratios for trace-level analytes. Furthermore, we refined per-peptide collision energy (CE) optimization, discovering that precursors with a charge state exceeding their basic amino acid count require unusually low energies for optimal fragmentation. This finding is of particular importance for the non-tryptic peptides characteristic of the immunopeptidome. We applied the optiPRM+ workflow to the challenging biological case of Human Papillomavirus type 16 (HPV16), a virus known to suppress antigen presentation pathways. This optimized strategy enabled the confident identification and validation of the HLA-A02:01-restricted epitope TIHDIILECV and the first MS-based detection of two novel viral targets: ISEYRHYCY (HLA-A01:01) and CVYCKQQLLR (HLA-A*11:01). To contextualize these findings, we performed global immunopeptidome analysis via DIA, which confirmed that these ultra-low abundance peptides were not detectable through untargeted methods despite being clearly validated by our targeted approach. By successfully detecting these viral peptides, we demonstrate that a systematically optimized targeted-first approach can uncover biologically relevant epitopes that remain invisible to conventional discovery-based 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