{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069749/checksum.txt"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069749/DC_RawData.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069749/DC_SpectrumMill_Results.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD069749/DC_MPP_Results.tar"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["george.katselis@usask.ca"],"submitter":["Daniel Chao"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"software":["Not available"],"submitter_keywords":["Brain","Rat","Lc-ms/ms"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD069749"],"tissue":["Brain"],"sample_protocol":["Protein digestion Prior to digestion, protein quantification was performed using the Pierce BCA Protein Assay Kit (ThermoFisher) according to the manufacturer's protocols. All samples were normalized to 2 mg/mL. In-solution digestion was performed using a protocol developed in our laboratory.16,17 Proteins were denatured using 50% trifluoroethanol (Fisher Scientific), followed by reduction with 10 mM dithiothreitol (MP Biomedicals) at 60 oC for 1 hour at 300 rpm (Eppendorf Thermomixer). To prevent reformation of disulphide bonds, 50 mM iodoacetamide (Fisher Scientific) was added, and samples were incubated in the absence of light at 37°C for 30 minutes at 500 rpm. Trifluoroethanol was then evaporated using a SpeedVac (Labconco) and incubated with cold acetone at -80 oC for 1 hour. Samples were then centrifuged at 13,000 rpm for 30 minutes at 4°C (Eppendorf 5430 R). The acetone supernatant was discarded and replaced with fresh cold acetone, followed by another incubation period at -80 oC for 1 hour and centrifugation at 13,000 rpm for 30 minutes at 4°C. The supernatant acetone was then removed via SpeedVac evaporation. The resulting precipitate was resuspended using 100 mM ammonium bicarbonate (Fisher Scientific). Trypsin/Lys-C buffer (50 ng/μL Trypsin/Lys-C in 0.1% acetic acid and 200mM ABC; Pierce) was added at a 1:40 enzyme-to-protein ratio, and samples were digested overnight at 37°C and 300 rpm. Samples were then evaporated using a SpeedVac and stored at -80°C. Desalting via Zip-tipping Samples were desalted using C18 Omix tips (Agilent) according to the following protocol. C18 tips were primed sequentially using 100% acetonitrile (ACN), 50% ACN and 50% water (H2O), then 0.1% trifluoroacetic acid (TFA) in H2O. Samples were reconstituted in a 3% ACN, 97% MS-grade H2O solution, and then adjusted to pH 3 using 2.5% TFA. Samples were loaded onto preconditioned tips by repeated aspiration and dispensing, then washed out with 0.1% TFA in MS-grade H2O. Bound peptides were eluted from the C18 tips sequentially through repeated aspiration and dispensing with 60 % ACN/0.1% formic acid (FA) and 70%ACN/0.1% FA. Eluates were combined, evaporated using the SpeedVac, and then stored at -80 °C awaiting proteomics analysis. LC-MS/MS Before mass spectrometric analysis, peptide samples were reconstituted in 30 μL of buffer (97:3:1, v/v/v; MS-grade water, acetonitrile, and formic acid; Fisher Scientific) and transferred to Agilent mass spectrometry vials. Comparative proteomics analyses were performed on an Agilent 6550 iFunnel quadrupole time-of-flight (QTOF) instrument equipped with an Agilent 1260 series liquid chromatography system and an Agilent Chip Cube LC–MS interface (Agilent Technologies, Canada). Chromatographic separation was achieved using a high-capacity Agilent HPLC Chip II: G4240–62030 Polaris-HR-Chip_3C18 containing a 360 nL enrichment column and a 75 μm × 150 mm analytical column, both packed with Polaris C18-A resin (180 Å, 3 μm stationary phase). Samples (2 μL) were first loaded onto the enrichment column with 0.1% formic acid in water at 2.0 μL/min, then transferred onto the analytical column. Peptides were separated with a linear gradient of solvent A (0.1% formic acid in water) and solvent B (0.1% formic acid in acetonitrile). The linear gradient was 3–25% B over 105 min, 25–40% B over 15 min, 40–90% B over 5 min, and held at 90% B for 5 min, at a flow rate of 0.3 μL/min. Positive ion electrospray ionization was performed with a capillary voltage of 1900 V, an ion fragmentor of 360 V, and nitrogen drying gas of 225 °C with a flow rate of 12 L/min. MS survey spectra were collected across a mass range of m/z 250–1700 at a scan rate of 8 spectra/s. MS/MS spectra were acquired across m/z 100–1700 with an isolation width of 1.3 amu."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Bioinformatics analysis The raw mass spectrometry data obtained from LC-MS/MS were extracted using the Spectrum Mill extractor (Agilent Technologies, Canada) with the following parameters - fixed modification: Carbamidomethylation (C); precursor MH+: 300 to 8000 Da; scan time range: 0 to 300 min; sequence tag length > 0; retention time (RT): +/- 120, m/z tolerance: +/- 0.05 m/z; precursor selection purity and spectral similarity as well as RT and m/z merging constraints; merge MS2 and MS2 spectra from same precursor; and 500 counts MS noise threshold. Extracted data was then searched against the SwissProt Rattus Norvegicus database (February 2025) using the Spectrum Mill search engine (Agilent Technologies, Canada). The search strategy consisted of 6 steps of searches with 2 auto-validation steps between each search. The search parameters that were fixed among all steps were as follows: 150 batch size, 2 cleavages missed max, monoisotopic masses, +/- 20 ppm precursor mass tolerance, +/- 50 ppm product mass tolerance, activated calculate reversed database scores, activated dynamic peak thresholding, score only discriminant scoring, -18 to 177 Da precursor mass shift range, and fixed modifications: Carbamidomethylation (C).   Step 1 parameters selected Lys-C/Tryp as the enzyme digest, variables modifications as the search mode, and the following variable modifications: carbamylated lysine, oxidized methionine, pyroglutamic acid, deamidated asparagine, phosphorylated serine, threonine, and tyrosine. Step 2 parameters selected Lys-C/Tryp as the enzyme digest and the same variable modifications as in Step 1, except that acetylated lysine was chosen instead of carbamylated lysine. The following steps were all conducted using the identity search mode. The third search step selected trypsin non-specific C-terminus as the enzyme digest. The fourth search step selected trypsin as the non-specific N-terminus enzyme digest. The fifth search step selected Lys-C non-specific C-terminus as the enzyme digest. The sixth search step selected Lys-C as the non-specific N-terminus enzyme digest. Auto-validation was performed between each searching step and consisted of two steps.  The first auto-validation step selected peptide mode, auto thresholds, 1.2% max false discovery rate (FDR) across each LC run, 2 to 7 precursor charge range, and 6 minimum sequence length. The second step of auto validation selected the protein polishing mode, auto thresholds, grouped proteins across all directories, set 1 as the minimum number of directories, 0 as the minimum protein score, and 1% as the threshold for automatically raising the minimum protein score to yield the maximum protein FDR. The two auto-validation steps were employed between each searching step and remained unchanged. Statistical Rationale Statistical analyses of our results were performed using Mass Profiler Professional software (Agilent Technologies, Canada). Analysis was performed based on the total spectral intensity of the proteins by summing the areas for each validated peptide. Spectral intensities were normalized based on protein concentration using an external scalar. The external scalar was calculated by dividing the protein concentration of each sample by the protein concentration of the lowest sample, as determined through quantification. Two parameters were used to evaluate our data: sex (female versus male) and exposure (0 Hz, 4 Hz, and 30 Hz). Normalized proteins were then filtered based on their abundance and frequency (must be present in all samples of at least one condition). Intensities were transformed using log2 and a two-way ANOVA with multiple hypothesis testing correction was performed. Multiple testing was controlled by Benjamini–Hochberg FDR (q < 0.05) and a list of statistically significant proteins (p < 0.001) with a fold change (FC) ≥ 10 was created. The stringent thresholds of p < 0.001 and a FC ≥ 10 were employed to ensure a high level of confidence in our results, thereby strengthening the validity of our findings.  Principal component analysis (PCA) was performed based on the differentially regulated proteins identified. The SwissProt database (www.uniprot.org) was used to determine the functions of differentially regulated proteins. STRING analysis (https://string-db.org/) was used to identify gene ontology (GO) categories of the differentially regulated proteins as well as to identify protein-protein interactions."],"omics_type":["Proteomics"],"labhead":["Dr. George S. Katselis"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Department of Medicine (CCRAH), College of Medicine, University of Saskatchewan"],"species":["Rattus Norvegicus (rat)"],"submitter_mail":["djc959@usask.ca"],"publication":["Not available"],"submitter_affiliation":["Health Sciences, College of Medicine, University of Saskatchewan"],"submitter_country":["Canada"],"additional_accession":[]},"is_claimable":false,"name":"Occupationally Relevant Vibrations and the Brain: Frequency-Dependent Proteomics Signatures in a Rat Model","description":"Occupational exposure to whole-body vibration (WBV), particularly in agricultural settings, has been linked to adverse cognitive and physiological outcomes. This study investigates the neurophysiological effects of WBV using a rat model exposed to sinusoidal vibrations at 4 Hz and 30 Hz, frequencies relevant to machinery operation. Forty-four Sprague-Dawley rats were randomly assigned to control (0 Hz), low-frequency (4 Hz), or high-frequency (30 Hz) vibration conditions. Following three days of exposure, brain tissues were harvested and analyzed using mass spectrometry-based proteomics to identify differentially expressed proteins.  Proteomics analysis revealed distinct frequency-dependent alterations in brain protein expression. A total of 32 cognition-related proteins were differentially regulated at 4 Hz compared to 0 Hz, 29 at 30 Hz compared to 0 Hz, and 13 between 4 Hz and 30 Hz. Principal component analysis demonstrated clear separation among groups, indicating unique proteomics signatures for each vibration condition. Functional enrichment and protein-protein interaction analyses revealed that differentially expressed proteins were involved in synaptic plasticity, cytoskeletal organization, calcium regulation, and neurotransmitter release. Notably, 4 Hz exposure was associated with upregulation of proteins linked to calcium homeostasis and synaptic integrity, suggesting potential cognitive disruption. In contrast, 30 Hz exposure resulted in the upregulation of proteins associated with axonal guidance and neuroprotection, indicating possible adaptive or beneficial effects. Comparative analysis between 4 Hz and 30 Hz conditions highlighted proteins such as syntaxin-1A and glutamate receptor 2, which may serve as biomarkers for cognitive impairment or resilience. This study provides novel insights into the biological mechanisms underlying WBV-induced cognitive changes and highlights the importance of vibration frequency in determining neurophysiological outcomes. These findings lay the groundwork for future research integrating proteomics with behavioral assessments to better understand the impact of WBV on brain function in both animals and 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