{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/20221003_PRI_ECL1_NEO1_50cm_uPACgen3_P170_R558_90min_DDA_S12.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/20221003_PRI_ECL1_NEO1_50cm_uPACgen3_P170_R558_90min_DDA_S10.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/20221003_PRI_ECL1_NEO1_50cm_uPACgen3_P170_R558_90min_DDA_S14.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/20221003_PRI_ECL1_NEO1_50cm_uPACgen3_P170_R558_90min_DDA_S16.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/20221003_PRI_ECL1_NEO1_50cm_uPACgen3_P170_R558_90min_DDA_S8.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/20221003_PRI_ECL1_NEO1_50cm_uPACgen3_P170_R558_90min_DDA_S3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/20221003_PRI_ECL1_NEO1_50cm_uPACgen3_P170_R558_90min_DDA_S6.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/20221003_PRI_ECL1_NEO1_50cm_uPACgen3_P170_R558_90min_DDA_S4.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/20221003_PRI_ECL1_NEO1_50cm_uPACgen3_P170_R558_90min_DDA_S1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/20221003_PRI_ECL1_NEO1_50cm_uPACgen3_P170_R558_90min_DDA_S13.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/20221003_PRI_ECL1_NEO1_50cm_uPACgen3_P170_R558_90min_DDA_S11.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/20221003_PRI_ECL1_NEO1_50cm_uPACgen3_P170_R558_90min_DDA_S2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/20221003_PRI_ECL1_NEO1_50cm_uPACgen3_P170_R558_90min_DDA_S9.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/20221003_PRI_ECL1_NEO1_50cm_uPACgen3_P170_R558_90min_DDA_S15.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/20221003_PRI_ECL1_NEO1_50cm_uPACgen3_P170_R558_90min_DDA_S5.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/20221003_PRI_ECL1_NEO1_50cm_uPACgen3_P170_R558_90min_DDA_S7.raw"],"Mzid":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/Pilot_Exp.mzid"],"Mgf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD078552/Pilot_Exp.MSMS.mgf"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"labhead_mail":["j.burniston@ljmu.ac.uk"],"submitter":["Jatin Burniston"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Human","Protein trunover","Skeletal muscle"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD078552"],"tissue":["Skeletal Muscle"],"sample_protocol":["Muscle tissue samples were lysed with lysis buffer (1% (w/v) Sodium Deoxycholate, 100 mM TEAB, pH 8.5) in a 96-well BeatBox tissue homogenizer (Preomics) for 10 min at standard setting, followed by incubation for 10 min at 95°C. BeatBox homogenization and boiling were repeated for a total of five rounds. TCEP (Thermo Fisher Scientific, CAT #77720) was added to 5mM, and CAA (Sigma Aldrich, CAT #22790-250G-F) to 20mM, and incubated at 45 °C for 20 min. Samples were digested by addition of Trypsin (Seq. Gr. Mod, Trypsin, bulk scale, Promega, CAT # V511X) and Lys-C (Lysine C, Fujifilm, CAT #129-02541) at 1:100 enzyme/protein ratio. Peptides were desalted using iST plates (iST Positive Pressure Plate 96x, Preomics, CAT # SFG00084), dried down, and resuspended in buffer A* (2% ACN, 0.1% TFA) for LC-MS analysis.  Peptides were separated on a 50 cm uPAC Gen3 column with a Vanquish Neo HPLC system (Thermo Fisher Scientific) coupled through a nano-electrospray source to a Tribrid Eclipse mass spectrometer (Thermo Fisher Scientific) with a non-linear gradient of 4 – 45 % buffer B (0.1 % formic acid, 80 % acetonitrile) at a flow rate of 250 nL/min over 90min. The column temperature was kept at 50° C. Samples were acquired using a DDA MS2 data acquisition, where the Tribrid mass spectrometer was switching between a full scan (120 K resolution, 50ms max. injection time, AGC target 100%), to a data‐dependent (Top-20) MS/MS scans in the Orbitrap analyser (15K resolution, 22 ms max. injection time, AGC target 200%). Isolation window was set to 1.4 (m/z), and normalized collision energy to 30. Precursors were filtered by charge state of 2-6 and multiple sequencing of peptides was minimized by excluding the selected peptide candidates for 60 s."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Protein abundances were measured by label-free quantitation using Progenesis Quantitative Informatics for Proteomics (QI-P; Nonlinear Dynamics, Waters Corp., Newcastle, UK, Version 4.2), consistent with previous studies (Burniston et al. 2014; Camera et al. 2017; Burniston 2019; Hesketh et al. 2020). Log-transformed MS data were normalized by inter-sample abundance ratio, and relative protein abundances were calculated using nonconflicting peptides only. MS/MS spectra were exported in Mascot generic format and searched against the Swiss-Prot database (2021_03) restricted to Homo-sapiens (20,371 sequences) using locally implemented Mascot server (v.2.8; www.matrixscience.com). The enzyme specificity was trypsin with 2 allowed missed cleavages, carbamidomethylation of cysteine (fixed modification) and oxidation of methionine (variable modification). MS data were searched with m/z error tolerances of 10 ppm for peptide ions and 0.6 Da for fragment ion spectra. Peptide results were filtered to 1 % FDR based on decoy search and at least 1 unique peptide was required to identify each protein. The Mascot output (xml format), restricted to non-homologous protein identifications was recombined with MS profile data in Progenesis."],"omics_type":["Proteomics"],"labhead":["Prof Jatin G Burniston"],"instrument_platform":[""],"labhead_affiliation":["Liverpool John Moores University"],"submission_type":["COMPLETE"],"species":["Homo Sapiens (human)"],"submitter_mail":["j.burniston@ljmu.ac.uk"],"publication":["42421643 Højfeldt G, Helge BW, van Hall G, Schjerling P, Kjær M, Mackey AL, Burniston JG, Agergaard J. &lt;sup&gt;2&lt;/sup&gt;H&lt;sub&gt;2&lt;/sub&gt;O labeling methods for bulk and single muscle protein synthesis measures, and measures of integrated muscle protein synthesis and breakdown rates: A pilot study. Physiol Rep. 2026 14(13):e71013 10.14814/phy2.71013"],"submitter_affiliation":["Liverpool John Moores University"],"submitter_country":["United Kingdom"],"doi":["10.6019/PXD078552"],"pubmed_abstract":["This methodological pilot study explored the feasibility of an integrated tracer approach for simultaneous measurement of human skeletal muscle protein synthesis and breakdown during prolonged deuterium oxide (<sup>2</sup>H<sub>2</sub>O) labeling. Four healthy men completed a five-week protocol combining daily oral <sup>2</sup>H<sub>2</sub>O intake with selected stable isotope amino acid tracers to assess bulk fractional synthesis rates, fractional breakdown rates, and single-protein turnover. The study specifically addressed the methodological question of whether bulk or individual protein synthesis measurements remain consistent over a prolonged <sup>2</sup>H<sub>2</sub>O labeling period. We suggest that measurements of mixed-protein fractions in muscle might be vulnerable to error due to the rise-to-plateau kinetics associated with longer-duration labeling. Mean mixed-protein synthesis rates could be underestimated when labeling exceeds approximately 4 weeks. Increasing precursor enrichment mitigated this effect but highlights the need for controlled enrichment strategies in long-term studies. In contrast, dynamic proteome profiling (DPP) provided more robust single-protein turnover estimates across the full period because the different isotopic plateaus of individual peptides could be modeled. The study also tested the feasibility of combining <sup>2</sup>H<sub>2</sub>O labeling with <sup>15</sup>N-alanine-based breakdown measurements and evaluated potential interference from multiple tracers on DPP outputs. Together, these findings outline practical considerations, limitations, and feasibility of an integrated multi-tracer framework for studying human muscle protein turnover over extended periods."],"pubmed_title":["&lt;sup&gt;2&lt;/sup&gt;H&lt;sub&gt;2&lt;/sub&gt;O labeling methods for bulk and single muscle protein synthesis measures, and measures of integrated muscle protein synthesis and breakdown rates: A pilot study."],"pubmed_authors":["Højfeldt Grith G, Helge Bjørk Wulff BW, van Hall Gerrit G, Schjerling Peter P, Kjær Michael M, Mackey Abigail L AL, Burniston Jatin G JG, Agergaard Jakob J"],"additional_accession":[]},"is_claimable":false,"name":"Deuterium oxide labeling methods for bulk and single muscle protein synthesis measures, and measures of integrated muscle protein synthesis and breakdown rates","description":"This methodological pilot study explored the feasibility of an integrated tracer approach for simultaneous measurement of human skeletal muscle protein synthesis and breakdown during prolonged deuterium oxide (²H₂O) labelling. Four healthy men completed a five week protocol combining daily oral ²H₂O intake with selected stable isotope amino acid tracers to assess bulk fractional synthesis rates, fractional breakdown rates, and single protein turnover. The study specifically addressed the methodological question whether bulk or individual protein synthesis measurements remain consistent over a prolonged 2H₂O labelling period. We demonstrate that measurements of mixed-protein fractions in muscle are vulnerable to error due to the rise-to-plateau kinetics associated with longer-duration labelling. Mean mixed-protein synthesis rates can be underestimated when labelling exceeds approximately four weeks. Increasing precursor enrichment mitigated this effect but highlights the need for controlled enrichment strategies in long term studies. In contrast, dynamic proteome profiling (DPP) provided more robust single protein turnover estimates across the full period because the different isotopic plateaus of individual peptides could be modelled. The study also tested the feasibility of combining ²H₂O labelling with ¹⁵N alanine–based breakdown measurements and evaluated potential interference from multiple tracers on DPP outputs. Together, these findings outline practical considerations, limitations, and feasibility of an integrated multi tracer framework for studying human muscle protein turnover over extended 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