{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/files_list.xlsx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/Vitreous_mouse_WTvsCD11bKO_TMT_searchresults_Swissprot19.xlsx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/Vitreous_mouse_WTvsCD11bKO_labelfree_searchresults_Swissprot19.xlsx"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211118-29_FTMSms2hcd.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211118-31_FTMSms2hcd.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211118-27_FTMSms2hcd.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211118-16_FTMSms2hcd.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211118-23_FTMSms2hcd.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211022-05.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211118-22_FTMSms2hcd.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211118-19_FTMSms2hcd.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211118-25_FTMSms2hcd.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211022-03.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211118-20_FTMSms2hcd.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211118-17_FTMSms2hcd.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211118-30_FTMSms2hcd.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211118-28_FTMSms2hcd.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211118-21_FTMSms2hcd.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20210915-07.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211118-24_FTMSms2hcd.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20210915-05.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211118-26_FTMSms2hcd.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD045885/S20211118-18_FTMSms2hcd.raw"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["rgiger@umich.edu"],"submitter":["Juan Oses-Prieto"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"software":["Not available"],"submitter_keywords":["Vitreous","Itgam.","Mouse","Label free","Tmt","Cd11b"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD045885"],"tissue":["Vitreous Humor"],"sample_protocol":["Aliquots of vitreous samples (from n= 8 WT or n= 8 Itgam-/- mice) were digested with trypsin for proteomic analysis. Samples (100 µg protein) were resuspended at a concentration of 4 mg/ml in a solution containing 8M Guanidinium Hydrochloride (GndHCl), 100 mM ammonium bicarbonate and 10 mM tris(2-carboxyethyl)phosphine and incubated for 1h at 56ºC. This was followed by addition of 20 mM iodoacetamide and a 30-minute incubation at room temperature in the dark. The samples were then diluted with 100 mM ammonium bicarbonate to 1M GndHCl and protein concentration 0.5 mg/ml. For digestion, the samples were then added 2% (W/W) Lysyl Endopeptidase®, Mass Spectrometry Grade (Lys-C) (FUJIFILM Wako Chemicals U.S.A. Corporation) and incubated at 37°C on a rotator overnight. After that, samples were added to 2% (W/W) trypsin MS grade (Pierce- Thermo Fisher) and digested for 6 additional hours. After this, samples were acidified with formic acid to a final concentration of 5% formic, and the digests were then desalted using OMIX C18 pipette tips (Agilent) following the manufacturer’s protocol. OMIX eluates were dry-evaporated in preparation for direct “label free” MS analysis or for labeling with tandem mass tag (TMT) reagents for quantitative comparison. For TMT labeling, digested vitreous proteins were labeled according to the TMT 10plex kit instructions (ThermoFisher Scientific). Protein levels in WT and Itgam-/- vitreous were compared by TMT in triplicates, using 25 µg of digested protein per TMT channel. Combined, TMT labeled sample was fractionated on an AKTA purifier system utilizing a Phenomenex Gemini 3u C18 110A 100 x 1.0 mm column, operating at a flow rate of 0.080 mL/min. Buffer A consisted of 20 mM ammonium formate (pH 10), and buffer B consisted of 20 mM ammonium formate in 90% acetonitrile. Gradient details were as follows: 1 % to 30% B in 95 min, 30% B to 70% B in 12.5 min, 70% B back down to 1% B in 25 min. 0.27 mL fractions were collected, evaporated, and resuspended in 0.1% formic for mass spectrometry analysis."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Data were searched against the mouse subset of the SwissProt database (SwissProt.2019.07.31, 17026 entries searched), using Protein Prospector  with the following parameters: Enzyme specificity was set as Trypsin, and up to 2 missed cleavages per peptide were allowed. Carbamidomethylation of cysteine residues, and, in the case of TMT labelled samples, TMT10plex labeling of lysine residues and N-terminus of the protein were allowed as fixed modifications. N-acetylation of the N-terminus of the protein, loss of protein N-terminal methionine, pyroglutamate formation from of peptide N-terminal glutamines, oxidation of methionine were allowed as variable modifications. Mass tolerance was 10 ppm in MS and 30 ppm in MS/MS. The false positive rate was estimated by searching the data using a concatenated database which contains the original SwissProt database, as well as a version of each original entry where the sequence has been randomized. A 1% FDR was permitted at the protein and peptide level. For quantitation only unique peptides were considered; peptides common to several proteins were not used for quantitative analysis. For TMT based quantitation, relative quantization of peptide abundance was performed via calculation of the intensity of reporter ions corresponding to the different TMT labels, present in MS/MS spectra. Intensities were determined by Protein Prospector. Median intensities of the reporter ions (each TMT channel) for all peptide spectral matches (PSMs) were used to normalize individual (sample specific) intensity values. For each PSM, relative abundances were calculated as ratios vs the average intensity levels in the 3 channels corresponding to control (WT) samples. For total protein relative levels, peptide ratios were aggregated to the protein levels using median values of the log2 ratios. Statistical significance was calculated comparing the values for the 3 technical replicates of WT and Itgam-/- samples in the TMT experiment with a 2-tailed t-test.   For label free quantitation, all spectra identified as matches to peptides of a given protein were reported, and the number of spectra (Peptide Spectral Matches, PSMs) used for label free quantitation of protein abundance in the samples. Relative abundance indexes were calculated as ratios of the PSMs vs the molecular weight of the polypeptide."],"omics_type":["Proteomics"],"labhead":["Roman J Giger"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Department of Cell and Developmental Biology, Neuroscience Graduate Program, Department of Neurology University of Michigan Medical School, Ann Arbor, MI 48109-2200"],"species":["Mus Musculus (mouse)"],"submitter_mail":["joses@cgl.ucsf.edu"],"publication":["38492223 Passino R, Finneran MC, Hafner H, Feng Q, Huffman LD, Zhao XF, Johnson CN, Kawaguchi R, Oses-Prieto JA, Burlingame AL, Geschwind DH, Benowitz LI, Giger RJ. Neutrophil-inflicted vasculature damage suppresses immune-mediated optic nerve regeneration. Cell Rep. 2024 43(3):113931 10.1016/j.celrep.2024.113931"],"submitter_affiliation":["UCSF"],"submitter_country":["United States"],"pubmed_abstract":["In adult mammals, injured retinal ganglion cells (RGCs) fail to spontaneously regrow severed axons, resulting in permanent visual deficits. Robust axon growth, however, is observed after intra-ocular injection of particulate β-glucan isolated from yeast. Blood-borne myeloid cells rapidly respond to β-glucan, releasing numerous pro-regenerative factors. Unfortunately, the pro-regenerative effects are undermined by retinal damage inflicted by an overactive immune system. Here, we demonstrate that protection of the inflamed vasculature promotes immune-mediated RGC regeneration. In the absence of microglia, leakiness of the blood-retina barrier increases, pro-inflammatory neutrophils are elevated, and RGC regeneration is reduced. Functional ablation of the complement receptor 3 (CD11b/integrin-αM), but not the complement components C1q<sup>-/-</sup> or C3<sup>-/-</sup>, reduces ocular inflammation, protects the blood-retina barrier, and enhances RGC regeneration. Selective targeting of neutrophils with anti-Ly6G does not increase axogenic neutrophils but protects the blood-retina barrier and enhances RGC regeneration. Together, these findings reveal that protection of the inflamed vasculature promotes neuronal regeneration."],"pubmed_title":["Neutrophil-inflicted vasculature damage suppresses immune-mediated optic nerve regeneration."],"pubmed_authors":["Passino Ryan R, Finneran Matthew C MC, Hafner Hannah H, Feng Qian Q, Huffman Lucas D LD, Zhao Xiao-Feng XF, Johnson Craig N CN, Kawaguchi Riki R, Oses-Prieto Juan A JA, Burlingame Alma L AL, Geschwind Daniel H DH, Benowitz Larry I LI, Giger Roman J RJ"],"additional_accession":[]},"is_claimable":false,"name":"Proteomic analysis of vitreous in WT and CD11b KO mice.","description":"Our data support that following optic nerve crush injury, ocular infiltration of immune cells causes damage to the retinal vasculature and compromises the integrity of the blood-retina barrier (BRB). Functional ablation of integrin alphaM (CD11b) attenuates immune cell trafficking, protects the BRB, and strongly enhances β-glucan-elicited retinal ganglion cells axon regeneration. Here, we performed an unbiased analysis of the vitreal proteome; we harvested vitreous humor from WT and Itgam-/- mice, β-glucan treated after optic nerve injury, and used mass spectrometry-based proteomics for differential analysis of the WT and Itgam-/- vitreous proteome (label free and tandem mass tagging).","dates":{"publication":"2026-08-05","submission":"2023-10-03"},"accession":"PXD045885","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:475174","NEWT:111205","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:10034","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:1589","NEWT:135622","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:383379","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:111225","NEWT:7719","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:3347","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:244366","NEWT:1246791","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2853422","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:95486","NEWT:1883446","NEWT:1233435","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:460523","NEWT:235443","NEWT:1757312","NEWT:85694","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:373153","NEWT:472","NEWT:940825","NEWT:529507","NEWT:1071661","NEWT:470","NEWT:5911","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:906914","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:51338","NEWT:575412","NEWT:28112","NEWT:6493","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:5147","NEWT:28108","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:298176","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:443906","NEWT:519","NEWT:2510939","NEWT:7394","NEWT:6063","NEWT:1328388","NEWT:1548728","NEWT:667127","NEWT:9557","NEWT:377586","NEWT:300641","NEWT:39655","NEWT:9554","NEWT:38323","NEWT:475932","NEWT:256318","NEWT:206411","NCBITaxon:6191","NEWT:229533","NEWT:214053","NEWT:80863","NEWT:90675","NEWT:52638","NEWT:57075","NEWT:1666905","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:1123869","NEWT:9544","NEWT:9545","NEWT:979","NEWT:7370","NEWT:83906","NEWT:99488","NEWT:1134506","NEWT:255470","NEWT:38783","NEWT:6426","NEWT:33090","NEWT:9935","NEWT:287889","NEWT:305959","NEWT:13489","NEWT:29829","NEWT:92867","NEWT:92866","NCBITaxon:3055","NEWT:51750","NEWT:202950","NEWT:295027","NCBITaxon:11320","NEWT:632957","NEWT:9925","NCBITaxon:9606","NEWT:90690","NEWT:1436183","NEWT:300273","NEWT:4232","NEWT:416348","NEWT:11298","NEWT:4236","NEWT:7742","NEWT:196627","NEWT:200308","NEWT:200302","NEWT:870435","NEWT:9913","NEWT:9915","NEWT:105841","NEWT:2666255","NEWT:999810","NCBITaxon:5693","NEWT:28995","NEWT:1392998","NEWT:380394","NEWT:2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