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Crasset"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Top-down proteomics"],"software":[""],"submitter_keywords":["snakebite envenoming","geo-graphical venom phenotypes","naja nigricollis","Venom variation","Venom variation; bitis arietans; naja nigricollis; snakebite envenoming; geo-graphical venom phenotypes","bitis arietans"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD073787"],"tissue":["Venom"],"sample_protocol":["Proteomic analysis of triplicate venom samples was done in the Laboratory of Mass Spectrometry (MS-Lab), MolSys Research Unit, Liege University, Belgium. Approxi-mately 10 µg of each lyophilized venom was dissolved in 13.5 µL of 50 mM NH4HCO3, pH 7.8. The samples were reduced with 1.35 µL of 110mM dithiothreitol (DTT) for 40 min at 56 °C under shaking at 600 rpm. Then, reduced samples were alkylated for 30 min at room temperature in the dark with 1.3 µL of 250mM iodoacetamide. After that, 1.8 µL of 110 mM dithiothreitol (DTT) was added for 10 min at room temperature in the dark to quench the reaction. The samples were then digested enzymatically using trypsin in two consecutive steps. The first step involved a 1:50 (trypsin:protein) ratio and was incubated overnight at 37 °C with shaking at 600 rpm. The second step was performed with a 1:100 ratio and incubation at 37 °C for 3 hours (shaking 600 rpm). Stop reactions were conducted by acidifying the medium with 10% TFA (final concentration). Finally, the digested sam-ples were dried under a speed vacuum. Before mass spectrometry analysis, the samples were suspended in 20 µL of 0.1% TFA for desalting on ZipTip pipette tips with C18 resin. The elution was performed by 20 µL of 0.1% TFA/ACN (50/50). Peptide solutions were injected on an Acquity UPLC MClass liquid chromatography system from Waters (UK) coupled with a timsTOFSCP instruments from Bruker (Bremen, Germany) using data independent acquisition (DIA). The LC instrument was in Trap Elute configuration with a 10µL loop, a Symmetry C18 trap column from Waters (AC-QUITY UPLC M-Class Symmetry C18 Trap Column, pore size: 100 Å, particle size: 5 µm, ID: 180 µm, length: 20 mm, Cat. No.: 186007496) followed by an analytic C18 column Au-roraGen3 Elite from IonOpticks (pore size: 120 Å, particle size: 1.7 µm, ID: 75 µm, length: 15cm, Cat. No.: 186007496) equipped with a CaptiveSpray emitter tip. The LC method involved a 3-minute trapping step at 2% ACN followed by an analytical gradient ramping from 2% to 40% ACN over 29 minutes. MClass system was connectedtoa timsTOF SCP instrument from Bruker (Bremen, Germany) using a CaptiveSpray interface for nanoESI ionization. Ion mobility and m/z values have been calibrated using Agilent TuneMix. Ion mobility separation was performed from 1/K0 from 0.75 to 1.25 V.s/cm² with a ramp of 150 ms and an accumulation time of 150 ms (duty cycle ≈ 100%). Samples were analyzed in positive mode in data-dependent acquisition (DDA) using Parallel Accumulation–Se-rial Fragmentation (PASEF). The number of PASEF ramps was set to 6 for a total cycle time of 1.1s. Only precursors with a charge between 2 and 5 are selected for MS/MS anal-ysis with a minimal intensity of 1000 cps. The target intensity was set to 15,000 cps. A precursor filter is applied in function of the m/z and the ion mobility value to target mul-ticharged peptide precursor ions for MS/MS analysis."],"repository":["Pride"],"modification":[""],"quantification_method":[""],"data_protocol":["Raw LC-IM-MS/MS data were processed using FragPipe (version 23.1; NesViLab, Alexey Nesvizhskii’s Proteome Bioinformatics Group). Protein identification for Naja venoms was performed against the “Elapidae AND Venom” database (97,831 sequences), whereas the “Viperidae AND Venom” database (35,433 sequences) was used for Bitis ven-oms. All databases were retrieved from UniProt, accessed on September 29th, 2025. Post-translational modifications (PTMs) were specified as follows: carbamidomethylation (C) as a fixed modification, and oxidation (M), acetylation (protein N-terminus), and deami-dation (N/Q) as variable modifications, with a maximum of 3, 1, and 1 occurrence(s), re-spectively. Enzymatic digestion was set to “strict trypsin”, allowing up to three missed cleavages. The precursor and fragment mass tolerances were both set to 20 ppm. PSM validation was performed using Percolator with the options -only-psms, -no-terminate, and -post-terminate-tdc. Protein inference was conducted using ProteinProphet with the command-line parameter -maxppmdiff 2000000. Label-free quantification (LFQ) was car-ried out with IonQuant, using MS1-based quantification. Both LFQ and MaxLFQ algo-rithms were enabled, with a minimum of one ion required for MaxLFQ quantification. Match-between-runs (MBR) and intensity normalization across runs were activated, and the MBR ion-level false discovery rate (FDR) was set to 0.01. Quantitative protein intensity values obtained from the FragPipe/IonQuant work-flow were imported into Perseus (v2.1.5.0) for downstream statistical analysis. Prior to analysis, the dataset was curated by removing common contaminants, reverse sequences, and proteins identified only by site, as exported by FragPipe. Proteins were retained only if quantified in, at least, 3 times in each group of replicates. MaxLFQ intensity values were subsequently log₂-transformed to stabilize variance. Missing values were handled using either imputation based on a downshifted Gauss-ian distribution (width=0.3, downshift = 1.8), following standard Perseus recommenda-tions to approximate low-abundance protein signals.To assess global variance structure and sample clustering, Principal Component Analysis (PCA) was performed on log₂-transformed, imputed LFQ intensity values. Data were mean-centered before PCA. Score plots were generated to visualize relationships between experimental conditions and de-tect potential outliers or batch effects. Differential Abundance Analysis (Pairwise compar-isons) between experimental groups (South vs North) were carried out using a two-sam-ple Student’s t-test (250 randomizations, FDR 0.05, S0 = 0.1). The resulting t-test statistics and fold-changes werevisualized using volcano plots, generated within Perseus, to high-light significantly up- and down-regulated proteins. All statistical analyses of proteomic data were conducted using explicitly defined prepro-cessing, normalization, and testing parameters to ensure reproducibility. Log₂-trans-formed LFQ intensity values were used throughout downstream analyses. Missing values were imputed using a downshifted Gaussian distribution (width = 0.3; downshift = 1.8), as implemented in Perseus, to approximate signals from low-abundance proteins. These parameters were selected according to standard Perseus recommendations for label-free proteomics. Principal Component Analysis (PCA) was performed on mean-centered, log₂-transformed and imputed LFQ intensities to visualize variance structure and sample re-lationships. PCA was applied as an exploratory multivariate approach rather than for population-level inference."],"omics_type":["Proteomics"],"labhead":["Quinton Loïc"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Laboratory of Mass Spectrometry, MolSys Research Unit, University of Liège, 4000 Liège, Belgium"],"species":["Bitis Arietans","Naja Nigricollis"],"publication":["42188623 Adeyi AO, Emmanuel OS, Itang SI, Ajisebiola BS, Kumar M, Rudresha GV, Gond PG, Crasset T, Redureau D, Amorim FG, Sunagar K, Quinton L. Preliminary Insights into Geographic Variation in Venom Profiles and Functional Activities of Nigerian Snakes, &lt;i&gt;Bitis arietans&lt;/i&gt; and &lt;i&gt;Naja nigricollis&lt;/i&gt;. Toxins (Basel). 2026 18(5):221 10.3390/toxins18050221"],"submitter_mail":["thomas.crasset@uliege.be"],"submitter_affiliation":["Mass Spectrometry Laboratory - University of Liège"],"submitter_country":["Belgium"],"pubmed_abstract":["Snakebite envenoming is a major yet neglected tropical disease in sub-Saharan Africa, where antivenom efficacy is critically limited by intraspecific venom variation shaped by local ecological pressures. Nigeria's sharply contrasting Sudan Savanna (North) and Lowland Rainforest (South) provide an ideal natural system to investigate this variation, yet a comparative analysis of its medically important snakes has been lacking. We conducted an integrated proteomic and functional characterization of venoms from the puff adder (<i>Bitis arietans</i>) and black-necked spitting cobra (<i>Naja nigricollis</i>) collected in Kaduna (North) and Ibadan (South). Using high-resolution LC-MS/MS, SDS-PAGE, and biochemical assays (phospholipase A<sub>2</sub>, protease, fibrinogenolytic, hemolytic, and coagulation activities), we mapped region-specific venom compositions and characterized their functional activities. <i>Bitis arietans</i> displayed region-associated divergence: southern venom was enriched in serine proteases, whereas northern venom was dominated by lectins and distinct snake venom metalloproteinase isoforms. <i>Naja nigricollis</i> showed a conserved phospholipase A<sub>2</sub>/three-finger toxins backbone, yet southern venoms exhibited elevated snake venom metalloproteinase III and L-amino acid oxidase. These molecular differences manifested functionally, with southern <i>B. arietans</i> venom showing higher protease activity than northern <i>B. arietans</i>, whereas southern and northern <i>N. nigricollis</i> venom exhibited similar protease activity but enhanced phospholipase A<sub>2</sub> activity in southern <i>N. nigricollis</i>. This work provides the first integrated proteomic and functional comparison of venoms from northern and southern Nigerian venom sample of <i>B. arietans</i> and <i>N. nigricollis</i>. While based on a limited number of individuals, the observed differences should be considered preliminary and indicative of potential regional trends rather than population-level characteristics."],"pubmed_title":["Preliminary Insights into Geographic Variation in Venom Profiles and Functional Activities of Nigerian Snakes, &lt;i&gt;Bitis arietans&lt;/i&gt; and &lt;i&gt;Naja nigricollis&lt;/i&gt;."],"pubmed_authors":["Adeyi Akindele Oluwatosin AO, Emmanuel Oluwatimilehin Stephen OS, Itang Samuel Itang SI, Ajisebiola Babafemi Siji BS, Kumar Mihir M, Rudresha Gotravalli V GV, Gond Prasad Gopalkrishna PG, Crasset Thomas T, Redureau Damien D, Amorim Fernanda Gobbi FG, Sunagar Kartik K, Quinton Loïc L"],"additional_accession":[]},"is_claimable":false,"name":"North vs. South: Ecoregion-Specific Variations of Venom Toxin Profiles and Functional Activities in Nigerian Bitis arietans and Naja nigricollis","description":"Snakebite envenoming is a major yet neglected tropical disease in sub-Saharan Africa, where antivenom efficacy is critically limited by intraspecific venom variation shaped by local'eco-logical pressures. Nigeria’s sharply contrasting Sudan Savanna (North) and Lowland Rainforest (South) provide an ideal natural system toinvestigate this variation, yet a comparative analysis of its medically important snakes has been lacking. We conducted an integrated proteomic and func-tional characterization of venoms from the puff adder (Bitis arietans) and black-necked spitting cobra (Naja nigricollis) collected in Kaduna (North) and Ibadan (South).Using high-resolution LC-MS/MS, SDS-PAGE, and biochemical assays (PLA₂, protease, fibrinogenolytic, haemolytic, and coagulation activities), we mapped region-specific venom compositions and corresponding toxic activities. Bitis arietans displayed striking ecoregion-driven divergence: southern populations were enriched in ser-ine proteases (27.54%), whereas northern venoms were dominated by lectins (25.4%) and distinct SVMP isoforms. Naja nigricollis showed a conserved PLA₂/3FTx backbone, yet southern venoms ex-hibited elevated SVMP III and LAAO abundance. These molecular differences manifested function-ally, with southern B. arietans showing significantly higher protease activity and southern N.nigricollis exhibiting enhanced PLA₂ activity. Principal component analysis suggested geography as a primary determinant of venom phenotype in both species. This work provides the first integrated proteomic and functional comparison of venoms from northern and southern Nigerian populations of Bitis arietans and Naja nigricollis. While based on a limited number of individuals, the observed differences reveal consistent regional trends that shouldbe interpreted as preliminary and hypoth-esis-generating rather than definitive population-level characteristics.","dates":{"publication":"2026-06-01","submission":"2026-01-29"},"accession":"PXD073787","cross_references":{"TAXONOMY":["NEWT:108018","NEWT:377960","NEWT:1131","NEWT:190486","NEWT:2737160","NEWT:2042546","NEWT:148942","NEWT:193528","NEWT:295546","NEWT:258594","NEWT:1126","NEWT:1129","NEWT:89187","NEWT:309807","NEWT:89184","NEWT:309800","NEWT:57577","NEWT:156563","NEWT:1323429","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:2315688","NEWT:44270","NEWT:592321","NEWT:1073882","NEWT:6819","NEWT:93217","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:32264","NEWT:10034","NEWT:10031","NEWT:82569","NEWT:661410","NEWT:488003","NEWT:224326","NEWT:376619","NEWT:3765","NEWT:2433","NEWT:1190602","NEWT:3767","NEWT:433727","NEWT:135622","NEWT:672127","NEWT:656061","NEWT:37965","NEWT:656064","NEWT:3760","NEWT:36630","NEWT:381198","NEWT:1176302","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:44250","NEWT:77151","NEWT:317447","NEWT:698761","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:1562698","NEWT:11308","NEWT:12637","NEWT:2164133","NEWT:1180","NEWT:2767846","NEWT:1343074","NEWT:314344","NEWT:108061","NEWT:143292","NEWT:2767842","NEWT:314345","NEWT:224308","NEWT:3134131","NEWT:49928","NEWT:160621","NEWT:110368","NCBITaxon:5204","NEWT:1916073","NEWT:1303873","NEWT:1310161","NEWT:1230383","NEWT:77133","NEWT:160620","NCBITaxon:77643","NEWT:1310165","NEWT:114727","NEWT:5516","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:1410384","NEWT:1310173","NEWT:1072569","NEWT:1072568","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:135666","NEWT:419481","NEWT:5507","NEWT:1140","NCBITaxon:2157","NEWT:2066563","NEWT:1143","NEWT:1336794","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:709964","NEWT:3710","NEWT:3712","NEWT:3711","NEWT:3714","NEWT:65121","NEWT:3716","NEWT:3715","NEWT:2065263","NEWT:1549675","NEWT:177437","NEWT:9014","NEWT:10891","NEWT:118221","NEWT:32201","NEWT:34869","NEWT:226126","NEWT:1616117","NEWT:34865","NEWT:28174","NEWT:550537","NEWT:284812","NEWT:284811","NEWT:3701","NEWT:3702","NEWT:1245466","NEWT:3704","NEWT:1246791","NEWT:34875","NEWT:10882","NEWT:1431297","NEWT:9005","NEWT:34871","NEWT:9006","NEWT:33548","NEWT:1883426","NEWT:657321","NEWT:1423687","NEWT:657322","NEWT:10886","NEWT:3707","NEWT:3708","NEWT:536231","NEWT:219813","NEWT:1301262","NEWT:319224","NEWT:2305479","NEWT:215451","NEWT:460519","NEWT:272843","NEWT:272844","NEWT:1348799","NEWT:55784","NEWT:485","NEWT:223074","NEWT:2499525","NEWT:467144","NEWT:142786","NEWT:28196","NEWT:2853422","NEWT:487","NEWT:1679718","NEWT:387344","NEWT:657318","NEWT:480","NEWT:67767","NEWT:46835","NEWT:216778","NEWT:376686","NEWT:237610","EFO:0001352","NEWT:219809","NEWT:219808","NEWT:119562","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:141469","NEWT:272831","NEWT:987059","NEWT:491","NEWT:422203","NEWT:460523","NEWT:2422","NEWT:2423","NEWT:3755","NEWT:85694","NEWT:85692","NEWT:911045","NEWT:3750","NEWT:1195466","NEWT:2483192","NEWT:85698","NEWT:291146","NEWT:233271","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:278161","NEWT:415978","NEWT:410289","NEWT:191701","NEWT:9054","NEWT:472","NEWT:29459","NEWT:34839","NEWT:476","NEWT:28128","NEWT:470","NEWT:41122","NEWT:1328300","NEWT:748693","NEWT:106299","NCBITaxon:50557","NEWT:63363","NEWT:3735","NEWT:29491","NEWT:911022","NEWT:446","NEWT:153481","NEWT:714485","NEWT:445","NEWT:427924","NEWT:2003758","NEWT:29486","NEWT:63366","NEWT:63367","NEWT:29488","NEWT:215402","NEWT:3726","NEWT:1120755","NEWT:1862567","NEWT:591090","NEWT:30455","NEWT:28141","NEWT:9030","NEWT:9031","NEWT:3728","NEWT:29471","NEWT:108931","NEWT:219799","NEWT:1325292","NEWT:219798","NEWT:548","NEWT:150475","NEWT:546","NEWT:1431340","NEWT:256737","NEWT:51350","NEWT:8694","NEWT:8692","NEWT:542","NEWT:394503","NEWT:13076","NEWT:219785","NEWT:451515","NEWT:8673","NEWT:550","NEWT:10804","NEWT:52694","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:42410","NEWT:40686","NEWT:1225786","NEWT:366497","NEWT:771870","NEWT:8665","NEWT:51338","NEWT:771875","NEWT:377142","NEWT:9995","NEWT:28112","NEWT:49012","NEWT:28110","NEWT:10832","NEWT:311339","NEWT:507601","NEWT:520","NEWT:64657","NEWT:186441","NEWT:2585209","NEWT:643680","NEWT:214092","NEWT:40697","NEWT:13095","NEWT:162425","NEWT:242124","NEWT:9986","NEWT:8654","NEWT:536","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:80833","NEWT:479096","NEWT:28108","NEWT:28104","NEWT:1114957","NEWT:568703","NEWT:568708","NEWT:480020","NEWT:51315","NEWT:52641","NEWT:353152","NEWT:116597","NEWT:353153","NEWT:116598","NEWT:227377","NEWT:1774284","NEWT:27689","NEWT:207769","NEWT:40674","NEWT:51329","NCBITaxon:1763","NEWT:443906","NEWT:6055","NEWT:13037","NEWT:518","NEWT:519","NEWT:941638","NEWT:511","NEWT:7394","NEWT:6063","NEWT:404330","NEWT:1328388","NEWT:13064","NEWT:529120","NEWT:7375","NEWT:300641","NEWT:39655","NEWT:38323","NEWT:206411","NEWT:80869","NEWT:214053","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