{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD059719/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD059719/allBeers.RAW.zip"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD059719/RESULTS_TXT_MQ_runs.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["k.scherf.leibniz-lsb@tum.de"],"submitter":["Eleonora Tissen"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"disease":["Celiac Disease"],"software":[""],"submitter_keywords":[""],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD059719"],"sample_protocol":["Two carboxylate-modified paramagnetic beads (hydrophilic and hydrophobic) were used for single-pot solid-phase-enhanced sample preparation (SP3). Before use, the two types of beads were combined in a ratio of 1:1 (v/v) and rinsed with water. After immobilizing the beads by incubation on a magnetic rack for 2 min, the supernatant was discarded, and beads were reconstituted in water at a concentration of 20 μg solids/μL or 50 µg solids/µL. The prepared bead mixes were stored at 4 °C. The SP3 digest was performed in triplicate for each beer according to the protocol by Sielaff et al. (2017) with slight adjustments. In brief, 50 µL of tris(hydroxymethyl)aminomethane-hydrochloride (TRIS-HCl, 0.5 mol/L, pH 8.5) was added to 250 µL of beer. Reduction and alkylation were performed by adding 35 µL of a combined solution containing tris(2-carboxyethyl)phosphine (TCEP, 0.1 mol/L in 0.5 mol/L TRIS-HCl, pH 8.5) and chloroacetamide (CAA, 0.4 mol/L in 0.5 mol/L TRIS-HCl, pH 8.5) and incubating for 1 h at 37 °C in the dark. The prepared bead mix (1–5 µL) was added to 80 µL of the reduced and alkylated beer to achieve a bead:protein ratio of 1:10. Before, the protein content of the beer samples was determined using the Pierce 660 nm Protein Assay (ThermoFisher Scientific, Darmstadt, Germany) according to the manufacturer’s instructions. Detailed information regarding the Pierce Assay can be found in the Supplement (Figure S1). Afterward, acetonitrile was added to a final concentration of 96% (v/v), and the samples were allowed to settle at 22 °C for 18 min. Subsequently, the beads were immobilized by incubation on a magnetic rack for 2 min. The supernatant was discarded, and the pellet was rinsed twice with acetonitrile, discarding the supernatant as the last step. Chymotrypsin hydrolysis (80–100 µL, enzyme:substrate ratio 1:25, in 0.05 mol/L ammonium bicarbonate, pH 8.0) was performed for 18 h at 37 °C in the dark. After overnight digestion, acetonitrile was added to reach a final concentration of 95% (v/v). The supernatant was removed after mixing and immobilizing the beads on the magnetic rack. Peptides bound to the beads were eluted using 100–400 µL of 2.5% (v/v) formic acid in water to achieve a final peptide concentration of approximately 30 ng/µL. The supernatant containing purified peptides was transferred into a fresh tube after immobilizing the beads on the magnetic rack and stored at -20 °C until analysis. Analysis was performed according to Geisslitz et al. (Geisslitz et al., 2022) with very slight modifications. An UltiMate 3000 RSLC nano system (ThermoFisher Scientific) was coupled to a Q Exactive Plus Orbitrap mass spectrometer (ThermoFisher Scientific). Peptide loading onto a trap column (Acclaim PepMap Neo 5 µm C18 300 µm × 5 mm nano-trap column; ThermoFisher Scientific) was performed for 5 min at a flow rate of 8 μL/min using water containing 2% acetonitrile and 0.1% formic acid. Subsequently, peptide separation was carried out on an analytical column (bioZen 2.6 µm Peptide XB-C18 Nano column, 250 mm × 0.075 mm, SecurityLink; Phenomenex, Torrance, CA, USA) under the following conditions: Solvent A consisted of 0.1% formic acid in water (v/v); solvent B consisted of 0.1% formic acid in acetonitrile (v/v). The flow rate was maintained at 300 nL/min at a column temperature of 40 °C using the following gradient: 2% B from 0 to 5 min, increasing to 5% B from 5 to 6 min, 5% to 20% B from 6 to 45 min, 20% to 33% B from 45 to 60 min, 33% to 100% B from 60 to 62 min, holding at 100% B from 62 to 65 min, followed by a decrease to 2% B from 65 to 66 min, and equilibration at 2% B until 80 min. The injection volume was adjusted for each sample to achieve a total protein amount of 200 ng per injection volume. The eluate from the analytical column was ionized using a Nanospray Flex Series ion source (ThermoFisher Scientific) in positive electrospray ionization (ESI+) mode. A source voltage of 1.8 kV at a capillary temperature of 250 °C and an S‐lens level of 60 was applied. The Q Exactive Plus mass spectrometer operated in data-dependent acquisition (DDA) mode, selecting the 20 most intense precursor ions from each MS1 full scan for fragmentation with an isolation width of 2.0 m/z at 28% normalized collision energy and default charge state of 2+. MS1 spectra were recorded in the Orbitrap within a mass range of m/z 360–1300 at a resolution of 70,000 (at m/z 200), with an automatic gain control (AGC) target of 3E6 and a maximum injection time of 50 ms. MS2 spectra were also acquired in the Orbitrap at a resolution of 17,500 for ions with charges ranging from 2+ to 7+, with an AGC target of 1E5, a maximum injection time of 50 ms, and a fixed first mass of m/z 140 and dynamic exclusion was set to 15 s. Data acquisition was performed with Xcalibur (ThermoFisher Scientific, version 4.2.47). The MS was calibrated weekly according to the manufacturer’s standard external calibration procedure prior to analysis."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Peptides were identified with the software MaxQuant (version 2.5.1.0) (Tyanova et al., 2016) by searching the MS raw data directly as input against two FASTA files of the UniProtKB (Bateman et al., 2024) database containing all entries from Hordeum vulgare (taxonomy: [4513], 55,751 entries, downloaded November 2022) and Triticum aestivum (taxonomy: [4565], 152,266 results, downloaded August 2023). The parameters were set as follows: digestion mode: specific; enzyme: chymotrypsin; maximum missed cleavage sites: 2; variable modifications: oxidation (M), Acetyl (Protein N-term); fixed modification: Carbamidomethyl (C); minimum peptide length: 7; max. peptide mass: 4600 Da; 1% peptide and protein false discovery rate. Match between runs was activated, and the matching time window was set to 0.4 min. Other parameters were set as default."],"omics_type":["Proteomics"],"labhead":["Katharina Scherf"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Leibniz Institute for Food Systems Biology at the Technical University of Munich"],"species":["Hordeum Vulgare (barley)","Triticum Aestivum (wheat)"],"submitter_mail":["e.tissen.leibniz-lsb@tum.de"],"publication":["10.1016/J.AFRES.2026.101952"],"submitter_affiliation":["Leibniz Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany"],"submitter_country":["Germany"],"additional_accession":[]},"is_claimable":false,"name":"Identification of celiac-disease active peptides in gluten-free beers by nanoLC-MS/MS","description":"Barley beers may be rendered gluten-free by specialized brewing processes. One controversial issue is whether these beers contain residual gluten peptides carrying at least one celiac disease (CeD)-active epitope, because routine methods to assess whether the beer is gluten-free like competitive enzyme-linked immunosorbent assays (ELISA) may fail to detect potentially harmful peptides. We used untargeted nano-liquid chromatography-tandem mass spectrometry (nanoLC MS/MS) to identify CeD-active peptides in 21 gluten-free barley beers and four regular or carbohydrate-reducedbeers. While the G12 ELISA confirmed gluten levels below 20 mg/kg in all gluten-free beers, the R5 ELISA detected gluten levels in four beers exceeding this threshold, highlighting method discrepancies. nanoLC-MS/MS identified 44 CeD active peptides in seven gluten-free and four non-gluten-free beers, of which 17 CeD-active peptides had no ELISA epitope and therefore escape detection. Accurate quantitation of thesepeptides combined with in vivo toxicity assessment will be needed to provide guidance on clinical 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