Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077831/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077831/Peptide.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077831/Protein.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077831/Rajagopal_004_5233_8141_01_20250218082335.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077831/Rajagopal_004_5233_8141_02_20250218134615.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077831/Rajagopal_004_5233_8141_02.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077831/Rajagopal_004_5233_8141_01.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077831/crap.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD077831/uniprot_sprot_human_2020_05.fastaprimaryOK200rajagopalr@wustl.eduRithwick RajagopalMass SpectrometryBottom-up proteomicsRetinal detachmentVitreousBiomarkerTmt-10-plexOcularProteomicsPvrProliferative vitreoretinopathyhttps://www.ebi.ac.uk/pride/archive/projects/PXD077831Vitreous HumorSurgical Technique and Sample Handling All participants underwent scheduled 23- or 25-gauge pars plana vitrectomy (PPV) under sterile operating room conditions. To ensure the integrity of the proteomic signature, a 1.0 mL undiluted vitreous biopsy was obtained at the initiation of the procedure, prior to the activation of the balanced salt solution infusion. Samples were immediately labeled and snap-frozen on dry ice before being transferred to long-term storage at -80°C. Peptide preparation and isobaric labeling A minimum sample of 150 L of each case and each control was submitted to the mass spectrometry lab for analysis. The samples were digested as previously described using a modification of the filter-aided sample preparation method.19 An equal volume of sodium dodecyl sulfate (SDS) buffer (5% SDS, 100mM Tris-HCl pH 8.0) was added to each vitreous sample to a final concentration of SDS of 2.5%. Samples were sonicated in the Covaris S220X using the following settings: peak incident power (PIP): 100, duty cycle (DC): 10%, cycles per burst (CPB): 500, time: 8 minutes. After determining protein concentration by Pierce™ BCA Protein Assay Kit (Pierce, part# 23225), 50 µg total protein were reduced by addition of 100 mM dithiothreitol (DTT) at 95 ºC for 10 minutes. A reference pool sample was also made from 15 µg of each sample in the study. The samples in SDT buffer (2.5 % SDS, 100 mM Tris-HCl, pH 8.0) were reduced by addition of 100 mM DTT at 95 ºC for 10 minutes. Reduced protein solutions were mixed with 400 µl of 100 mM Tris-HCL buffer, pH8.5 containing 8M urea (UA buffer) and transferred to the top chamber of a 30KDa filter unit (Millipore, part# MRCF0R030). The samples were spun in a microcentrifuge (Eppendorf, Model No. 5424) at 14,000 relative centrifugal force (rcf) for 20 minutes followed by an addition of 200 µL of UA buffer and centrifugation (14,000 rcf for 20 minutes). The flow-through was discarded and the proteins were alkylated by addition of 100 µl of 50 mM iodoacetamide in UA buffer to the top chamber of the filter unit. The samples were gyrated at 550 revolutions per minute (rpm) (Thermomixer, ThermoFisher Scientific) for 30 minutes at room temperature in the dark. The filter units were spun at 14,000 rcf for 20 minutes and the flow-through discarded. Two UA buffer centrifugation cycles were used to remove unreacted iodoacetamide and residual SDS. The urea buffer was exchanged with digestion buffer (50 mM ammonium bicarbonate buffer, pH 8.0) using one centrifugation cycles with 200 µl of the digestion buffer. The filters were transferred to a new collection tube and 80 µl of LysC (1 µAU) in 100 mM ammonium bicarbonate buffer (pH 8) was added. Samples were incubated for 2 hours at 37°C followed by the addition of trypsin (1:20) and incubation overnight at 37°C. Filter units were centrifuged at 14,000 rcf for 15 minutes to collect the peptides in the flow through. The filters were washed with 50 µl of 100 mM ammonium bicarbonate buffer and the wash was collected with the peptides. Peptides were acidified with trifluoroacetic acid (TFA) to a final concentration of 1% (vol/vol) and were desalted using 5 plug stage tips (C18).20 The peptides were eluted with 50% (vol/vol) acetonitrile (MeCN) in 0.1% (vol/vol) TFA and dried in a Speed-Vac (Thermo Scientific, Model No. Savant DNA 120 concentrator). Peptides were dissolved in 20 µl of 2% (vol/vol) MeCN in water. An aliquot (10%) was removed for quantification using the Pierce Quantitative Fluorometric Peptide Assay kit (Thermo Scientific, Cat. No. 23290). The equivalent volume of 1 µg of peptide from each sample and 2 µg of reference pool sample were transferred into a 0.5mL Eppendorf tube, dried in the Speed-Vac. Dried peptides were dissolved in 12 µl of HEPES buffer (100 mM, pH 8.0) (Sigma, H3537) and the peptides were labeled with tandem mass tag reagents (TMT10) (Thermo Scientific) according to manufacturer’s protocol. The labeled samples that were assigned to each ten-plex were pooled, dried, and dissolved in 120 µl of 1% formic acid (FA). The TMT10 labeled samples were desalted as described above for the unlabeled peptides. The eluates were transferred to autosampler vials (Sun-Sri, Cat. No. 200046), dried and stored at -80ºC for liquid chromatography-mass spectrometry (LC-MS) analysis.PrideNot availableNano-LC-MS/MS The samples in formic acid (1%) were loaded (2.5 µl) onto a 75 µXm i.d. × 50 cm Acclaim PepMap 100 C18 RSLC column (Thermo-Fisher Scientific) on an EASY nanoLC (Thermo Fisher Scientific) at a constant pressure of 700 bar at 100% A (1% FA). Prior to sample loading the column was equilibrated to 100% A for a total of 11 µl at 700 bar pressure. Peptide chromatography was initiated with mobile phase A (1% FA) containing 5% B (100% ACN, 1% FA) for 1 minute, then increased to 25% B over 195 minutes, to 35% B over 40 minutes, to 70% B in 6 minutes, to 95% B over 2 minutes and held at 95% B for 18 minutes, with a flow rate of 250 nL/minute. The data was acquired in data-dependent acquisition (DDA) mode. The full-scan mass spectra were acquired with the Orbitrap mass analyzer with a scan range of m/z = 350 to 1800 and a mass resolving power set to 70,000. Twelve data-dependent high-energy collisional dissociations were performed with a mass resolving power set to 35,000, a fixed lower value of m/z 100, an isolation width of 1.2 Da, and a normalized collision energy setting of 32. The maximum injection time was 60 ms for parent-ion analysis and 120 ms for product-ion analysis. The target ions that were selected for MS/MS were dynamically excluded for 40 seconds. The automatic gain control (AGC) was set at a target value of 3e6 ions for full MS scans and 1e5 ions for MS2 (fragmentation mass spectra of peptides selected in narrow mass range (2 Da) from MS1 scan). Peptide ions with charge states of one or ≥ 7 were excluded for high-energy collision-induced dissociation (HCD) acquisition. Protein Identification MS raw data were converted to peak lists using Proteome Discoverer (version 2.1.0.81, Thermo-Fischer Scientific) with the integration of reporter-ion intensities of TMT 10-plex at a mass tolerance of ±3.15 mDa.21 MS/MS spectra with charges greater than or equal to two were analyzed using Mascot search engine (Matrix Science, London, UK; version 2.7.0).22 Mascot was set up to search against a SwissProt database of human (version October 2020, 20,492 entries) and common contaminant proteins (cRAP, version 1.0 January 1st, 2012, 116 entries), assuming the digestion enzyme was trypsin/P with a maximum of 4 missed cleavages allowed. The searches were performed with a fragment ion mass tolerance of 0.02 Da and a parent ion tolerance of 20 ppm. Carbamidomethylation of cysteine was specified in Mascot as a fixed modification. Deamidation of asparagine, formation of pyro-glutamic acid from N-terminal glutamine, acetylation of protein N-terminus, oxidation of methionine, and pyro-carbamidomethylation of N-terminal cysteine were specified as variable modifications. Peptide spectrum matches (PSM) were filtered at 1% false-discovery rate (FDR) by searching against a reversed database and the ascribed peptide identities were accepted. The uniqueness of peptide sequences among the database entries was determined using the principal of parsimony. Protein identities were inferred from peptides using a greedy set cover algorithm from Mascot (spectral counting estimate by MASCOT: prot_empai) and the identities containing 2 Occam’s razor peptides were accepted. Protein Relative Quantification The processing, quality assurance and analysis of isobaric-labeled peptide LC-MS data were performed with proteoQ (version 1.5.0.0, https://github.com/qzhang503/proteoQ), software developed with the tidyverse approach (tidyverse R package version 1.3.1. https://CRAN.R-project.org/package=tidyverse) with open-source software for statistical computing and graphics. The reporter-ion intensities from each 10-plex or tandem mass tag (TMT) m/z values (channels) were converted to logarithmic ratios (base 2), relative to the average reporter-ion intensity of reference samples within each 10-plex. Within each sample, Dixon’s outlier removals were carried out recursively for peptides with greater than two identifying PSMs. The median of the ratios of PSM that could be assigned to the same peptide was first taken to represent the ratios of the incumbent peptide. The median of the ratios of peptides was then taken to represent the ratios of the inferred protein. To align protein ratios across samples, likelihood functions were first estimated for the log-ratios of proteins using finite mixture modeling, assuming two-component Gaussian mixtures.23 The ratio distributions were then aligned so that the maximum likelihood of log-ratios was centered at zero for each sample. Scaling normalization was performed to standardize the log-ratios of proteins across all samples. To reduce the influence of outliers from either log-ratios or reporter-ion intensities, the values between the 5th and 95th percentile of log-ratios and 5th and 95th percentile of intensity were used in the calculations of standard deviations.ProteomicsRithwick Rajagopal, MD, PhDJohn F. Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, Saint Louis, Missouri, United StatesPARTIALHomo Sapiens (human)Not availablerajagopalr@wustl.eduWashington University School of MedicineUnited StatesfalseThe baseline vitreous proteome in rhegmatogenous retinal detachment: a case–control study of proliferative vitreoretinopathyQuantitative proteomic analysis of undiluted human vitreous biopsies collected at the time of primary surgical repair of rhegmatogenous retinal detachment (RRD), comparing patients who later developed proliferative vitreoretinopathy (PVR; n=8) with matched RRD controls who did not (n=8). Vitreous samples were processed by S-Trap digestion, labeled with TMT 10-plex reagents, and analyzed by LC–MS/MS on a Thermo Q Exactive instrument (two TMT 10-plex sets, two LC-MS/MS injection replicates per set; four .raw files total). Identification and quantitation were performed using Mascot followed by the proteoQ R pipeline. The dataset comprises 879 quantified proteins after stringent contaminant filtering. The deposition is intended as a methodologically transparent reference dataset of the baseline RRD vitreous proteome for future 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