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Vasovic"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Hydrolysis","Lc-ms","Uio-66","Cleavage","Mofs","Protein"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD065039"],"sample_protocol":["HPLC-MS/MS measurements and pre-treatment of samples described under “Protein hydrolysis and elution samples” were performed by the Centre for Proteomics (CfP) at UAntwerp. The S-Trap micro spin column digestion protocol was performed to prepare the samples for analysis. 66.6 μL of each sample was diluted with tetraethylammonium bromide (TEAB, 200 mM) until a volume of 100 µL was reached, reduced using tris(2-carboxyethyl)phosphine (TCEP, 10 mM), and alkylated using 2- iodoacetamide (IAA, 19 mM). Phosphoric acid (85 % (w/v), 3.78 µl) and SDS (10 % (w/v), 21.4 µl) were added to get a final concentration of 2.5 % (w/v) and 2 % (w/v), respectively. Binding/washing buffer (794.1 µl) was added. 40 µl TEAB (50 mM) was added, and peptides were eluted. Elution was repeated with 40 µl formic acid (FA, 0.2 % (w/v)) and 40 µl acetonitrile (MeCN, 50 %), and all elutes were dried using a speedvac. Samples containing 1 µg of peptides dissolved in 10 µl of 2% ACN and 0.1% FA were separated on a Nano Acquity Ultra Performance LC system (Waters) fitted with a µPAC trapping column (Pharmafluidics) and  µPAC 200 cm column (Pharmafluidics). Each sample was injected twice to have technical duplicates of the different runs. The sample was loaded onto the trap column in 3 min at 10 µl/min in 94% solvent A 6% solvent B (solvent A is 0.1%FA in H 2 O, solvent B 0.1%FA in 80% ACN). The flow over the main column was 750 nL/min and the column was heated to 50°C. The run starts with a flow of 6% B and increases in 4 min to 15% B. The next 30 min the concentration of B increases to 50% and then to 94% in 5 min. After an isocratic flow of 3 min at 94% B, the concentration of B decreased in 5 min to 6% which was followed by 23 min of equilibration at 6% B. The nano-LC was coupled online with the mass spectrometer using a stainless-steel nano-bore Emitter (Thermo scientific) coupled to a Nanospray Flex ion source (Thermo Scientific). The Q Exactive Plus (Thermo Scientific) was used in data dependent analysis (DDA) method. The standard shotgun method was set up in MS/MS mode where a full scan spectrum (350–1850 m/z, resolution 70 000) was followed by a maximum of twenty HCD tandem mass spectra in the orbitrap, at a resolution of 17 500. A maximum inject time of 100 ms was set in the full MS, and 80 ms in MS2. The normalized collision energy used was and the minimal AGC target was set at 1.7 × 103. One run of technical duplicates was performed with the charge exclusion setting “unassigned, 1” and the collision energy set to 28. A second of technical duplicates run was performed with the charge exclusion setting “unassigned, 1” and the collision energy set to 32. An isolation window of 1.6 m/z and isolation offset of 0.3 m/z was applied. A dynamic exclusion list of 20 s was assigned."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Mass spectrometry data were processed using PEAKS Studio 12.5 (Bioinformatics Solutions Inc., Canada). MS/MS spectra were searched against a Uniprot Bos Taurus and the MaxQuant contaminant database. The search parameters included a parent mass tolerance of 10 ppm and fragment mass tolerance of 0.02 Da. Trypsin was specified as the digestion enzyme, allowing up to two missed cleavages. A semi-specific digestion mode was applied to enable detection of both tryptic and semi-tryptic peptides. Carbamidomethylation of cysteine was set as a fixed modification. Oxidation (M), deamidation (N, Q), and hydroxylation (P) were specified as variable modifications. Protein identifications were filtered with a minimum score of -10logP ≥ 20, at least one unique peptide per protein, and peptide-level false discovery rate (FDR) below 0.1%. Post-translational modifications were reported only when supported by a minimum ion intensity contribution of 2%. Further analyses were performed using R Statistical Software (v4.2.3), 2 Rstudio (v2024.12.1+563), 3 and the R packages shiny, 4 Biostrings 5 , readxl, 6 writexl, 7 seqinr 8 , shinyjs 9 for aligning protein peaks to the reference sequence and subsequently counting the amino acid ends."],"omics_type":["Proteomics"],"labhead":["prof. dr"],"instrument_platform":[""],"labhead_affiliation":["Full professor at Department of Chemistry, Celestijnenlaan 200f - box 2404 3001 Leuven"],"submission_type":["COMPLETE"],"species":["Bos Taurus (bovine)"],"submitter_mail":["tamara.vasovic@gmail.com"],"publication":["10.1021/ACS.CHEMMATER.6C00428"],"submitter_affiliation":["University of Belgade - Faculty of Chemistry"],"submitter_country":["Serbia"],"doi":["10.6019/PXD065039"],"additional_accession":[]},"is_claimable":false,"name":"Proteomics data for - Unravelling the mechanism of selective protein hydrolysis by metal-organic frameworks","description":"Metal-organic frameworks (MOFs) are emerging as alternatives to enzymes for selective peptide bond cleavage, which is a crucial procedure in proteomics, protein engineering, and proteolytic drug design. However, the limited understanding behind MOF-assisted protein interactions and hydrolysis mechanisms still severely hinder their development and application. Herein, we explore for the first time the synergy between interactions and reactivity of MOFs towards a whole protein, using both mass spectrometry and molecular docking calculations to understand the cleavage selectivity of UiO-66 towards bovine cytochrome c and hemoglobin and horse myoglobin. Our findings demonstrate that UiO-66 preferentially cleaves peptide bond containing glycine, threonine, and lysine due to the H-bonding and electrostatic interactions between the (positively-charged) “recruiting” residues on the protein surface and linker molecules on the surface of the MOF. This preference is drastically different from the aspartic acid selectivity observed with other Zr-based nanomaterials, and highlights the importance of MOF’s hybrid 3D framework to deliver cleavage specificity in the development of the next generation of MOF-based nanozymes for protein-based fields such as proteomics,biocatalysis and related areas.","dates":{"publication":"2026-04-09","submission":"2025-06-16"},"accession":"PXD065039","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NEWT:625351","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:57577","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:6819","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:3765","NEWT:1589","NEWT:135622","NEWT:67352","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:1582","NEWT:36630","NEWT:383379","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:1392488","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:29064","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:273791","NEWT:3347","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:410658","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:33554","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:44685","NEWT:161934","NEWT:156587","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:150808","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:3714","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:28174","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:66440","NEWT:1245466","NEWT:3704","NEWT:244366","NEWT:1246791","NEWT:176597","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:34878","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:1348799","NEWT:33995","NEWT:55784","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2499525","NEWT:2853422","NEWT:487","NEWT:1538553","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:237610","NEWT:95486","NEWT:119562","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:11757","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:491","NEWT:460523","NEWT:45954","NEWT:235443","NEWT:1757312","NEWT:85694","NEWT:109786","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:1640278","NEWT:472","NEWT:940825","NEWT:529507","NEWT:1071661","NEWT:28128","NEWT:470","NEWT:5911","NEWT:748693","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:3728","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:207340","NEWT:172271","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:771870","NEWT:51338","NEWT:575412","NEWT:28112","NEWT:6493","NEWT:10832","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:1613","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:298176","NEWT:353153","NEWT:227377","NEWT:1774284","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:443906","NEWT:519","NEWT:2510939","NEWT:7394","NEWT:6063","NEWT:1328388","NEWT:105487","NEWT:1548728","NEWT:667127","NEWT:9557","NEWT:377586","NEWT:7375","NEWT:300641","NEWT:39655","NEWT:9554","NEWT:38323","NEWT:475932","NEWT:256318","NEWT:206411","NCBITaxon:6191","NEWT:229533","NEWT:2925","NEWT:214053","NEWT:28550","NEWT:80863","NEWT:90675","NEWT:52639","NEWT:52638","NEWT:57075","NEW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