{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077479/checksum.txt"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077479/CALM_BOVIN.fasta"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077479/250823_CalM_MF_10-1000s.DnX","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077479/251120_CalM_MF_10-100ms.DnX","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077479/HDX_MF_CaM.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["E.Reading@soton.ac.uk"],"submitter":["Alistair Bailey"],"technology_type":["Mass Spectrometry","Bottom-up proteomics","MSE"],"software":["Not available"],"submitter_keywords":["Hdx-ms","Calmodulin","Droplet microfluidics"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD077479"],"sample_protocol":["Calmodulin (CaM, from bovine testes Cat No. P1431-1MG, Merck) was solubilised at 1 mg/mL in equilibration buffer (20 mM HEPES, pH 7.4). To prepare Ca2+-free CaM samples, 1 mM ethylenediaminetetraacetic acid (EDTA) was added to the CaM and incubated for 16 hours at room temperature. CaM dynamics was investigated with and without Ca2+ to characterise protein states at millisecond to second time scales (10 and 100 millisecond microfluidic, and 10, 100 and 1000 seconds manual labelling). Ca2+-bound CaM was prepared by adding 1 mM CaCl2 and incubation at room temperature (22 °C) for at least 3 hours prior to deuterium labelling. For CaM without Ca2+ all buffers were also equilibrated to room temperature. After equilibration, the exchange reaction was initiated by 10-fold dilution into deuterated labelling buffer (20 mM HEPES, pHread 7.0), yielding a 90% deuterium content in the final reaction mixture. Ca2+-bound CaM was deuterated with Ca2+-labelling buffer (20 mM HEPES, 1 mM CaCl2, pHread 7.0). To deuterate Ca2+-free CaM samples, Ca2+-free labelling buffer (20 mM HEPES, pHread 7.0) was applied. Reactions were quenched by 1:1 dilution with quench buffer (100 mM NaH2PO4, pH 2.3). Samples incubated for millisecond time scales (10 and 100 milliseconds) were processed as described above (microfluidic operation), with the exception of 8 second transport times from device to dry ice. 10, 100 and 1000 second labelling was performed manually bby introducing labelling and then quench buffer to the aliquoted samples. All protein states and labelling time points were performed in three technical replicates on two occasions. Samples processed by microfluidic and manual methods were stored at -80 °C for a maximum of 24 hours prior to mass spectrometry. Of note, when performing similar Ca2+-stripping procedures on bovine CaM recombinantly expressed in Escherchia coli (sourced from Cat No. C4874-1MG, Merck) then insignifcant differences between intended apo and holo states was observed within our HDX-MS analysis (data included in data repository PXD063880). With the apo state presenting as holo state, suggesting cation-stripping is more challenging from this construct and supports the value in exploring replication on proteins sourced from different cell type (or species) (Moroco & Engen, 2015).  Measurements were performed on an ACQUITY UPLC M-Class System with HDX Technology (Waters, Wilmslow, UK) directly coupled to a Xevo G2-XS QTof Mass Spectrometer (Waters, Wilmslow, UK). Frozen samples were quickly thawed, and the aqueous phase (top layer) was injected into the HDX manager. Samples obtained after automated D2O labelling were injected by the LEAP PAL robot directly after quench. Proteins were digested on-line using a self-packed pepsin (immobilized pepsin agarose resin, Cat No. 20343, Thermo Fisher) column (2.0 mm ID x 2 cm unpacked; Part No. C-130B) at 15°C, and resulting peptides were trapped/washed on an Acquity UPLC BEH C18 VanGuard pre-column (1.7 µm, 2.1 mm x 5 mm, Waters, Wilmslow, UK) for 3 min at 200 µL/min. The self-packed pepsin column was replaced by a union for samples containing pre-digested calmodulin (i.e. all samples from forward exchange experiments). Peptides were eluted and separated on an Acquity UPLC BEH C18 analytical column (1.7 µm, 1.0 mm x 100 mm, Waters, Wilmslow, UK) with a linear gradient over 7.5 minutes from 8 to 35% solvent B (0.23% formic acid in acetonitrile) at a flow rate of 40 µL/min and at 0°C. To prevent peptide carryover, the pepsin column was washed twice during the linear gradient using a pepsin wash solution (1.6 M guanidine-HCl, 4% acetonitrile, and 0.8% formic acid, pH 2.5). Further, chromatographic columns were washed after each sample run by applying a saw-tooth gradient."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["For peptide identification, undeuterated calmodulin was injected into the system applying the same settings for protein digestion and chromatographic separation. Peptides were measured in positive ion mode and MSE analysis was applied with a ramped collision energy from 20 to 45 V. Sodium iodide and leucine enkephalin were used for calibration and mass accuracy correction, respectively. Raw data from MSE runs were analyzed with ProteinLynx Global Server (PLGS) 3.0 (Waters, Wilmslow, UK). Identified peptides were loaded into DynamX 3.0 (Waters, Wilmslow, UK) and filtered as follows: minimum intensity: 1481, sequence length: 5–25, minimum products per amino acid: 0.11, minimum consecutive products: 1, minimum score: 6.62, maximum MH+ error: 10 ppm, file threshold: 4 out of 5 measurements. Peptides were manually curated to exclude MS traces of poor quality or false identifications. Subsequently, raw data from deuterated samples (with and without Ca2+ and non-equilibrium) were loaded to calculate the deuterium uptake at peptide level. To determine statistically significant differences in deuterium uptake between two protein states, a global 99% confidence threshold was calculated based on a previous approach including recently proposed corrections.  The uploaded data are the raw files, and processed Waters DynamX outputs associated the differential uptake experiments (Figure 5 in the manuscript).The Bovine calmodulin sequence is provided as a fasta file."],"omics_type":["Proteomics"],"labhead":["Eamonn Reading"],"instrument_platform":[""],"labhead_affiliation":["School of Biological Sciences, Building 85, University of Southampton, Southampton, SO17 1BJ"],"submission_type":["PARTIAL"],"species":["Bos Taurus (bovine)"],"publication":["Not available"],"submitter_mail":["ab604@soton.ac.uk"],"submitter_affiliation":["University of Southampton"],"submitter_country":["United Kingdom"],"additional_accession":[]},"is_claimable":false,"name":"Droplet microfluidic hydrogen/deuterium exchange for investigating protein dynamics with millisecond precision exchange","description":"Hydrogen/deuterium exchange (HDX) methods for studying protein dynamics would benefit from millisecond-scale incubations to probe intrinsically disordered proteins, highly dynamic regions and conformation changes. Here we investigate droplet microfluidics for rapid mixing to trigger D2O labelling, uniform incubations and rapid droplet merging for acid quenching in advance of mass spectrometry. A surfactant-free merging approach combining expansion elements for synchronised droplet collision proved robust. The high diffusive flux of D2O and protons enable microsecond mixing to trigger and arrest D2O labelling, respectively, affording the possibility of single millisecond incubations. Droplet HDX processors were used to measure the fast uptake characteristics of a model peptide. Forward exchange measurements demonstrate D2O labelling to be the rate-limiting step, in essence defining 10 milliseconds as the minimum practical incubation time for proteins in typical physiological conditions. With the ability to access millisecond time scales the fast dynamics of calmodulin, a model of calcium-triggered allostery with rapid conformational switching, was investigated. At 10 milliseconds, we could observe significant deuterium uptake within the well-defined EF-hand motifs (Ca2+ binding sites). These findings demonstrate millisecond HDX enabled by droplet microfluidics allows areas of heightened plasticity to be detected within a stably folded 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