Venomics

13 workflows · 2014–2025

Venomics: Venom from snakes, spiders, scorpions, ants and cone snails, where the species has no sequenced genome and the toxins are heavily modified. 13 catalogued workflows and 13 papers.

Venom from snakes, spiders, scorpions, ants and cone snails, where the species has no sequenced genome and the toxins are heavily modified.

Workflows 13
Papers 13
Authors 85
Active 2014-05-01 to 2025-08-23

Workflows (13)

  • Spider venom peptidome (SPITC + de novo) (2014): SPITC N-terminal derivatization + 18O labeling coupled with de novo peptide sequencing to simultaneously identify and quantify spider-venom peptides from species with unknown genomes.
  • Bothriopsis taeniata PLA2 K49 (2015): Automatic de novo sequencing (PEAKS Studio) with CID/HCD/ETD triplex MS/MS to elucidate the full-length sequence of a new PLA2 K49 (Btt-TX) from Bothriopsis taeniata snake venom.
  • Bufo gargarizans skin peptidome (2018): Peptidomics workflow using nano-LC-MS/MS and PEAKS de novo sequencing against a transcriptome-derived database to characterise <10 kDa bioactive peptides from Bufo gargarizans (Venenum Bufonis) skin secretions.
  • Hypnale hypnale venomics (2018): Venomics workflow combining SDS-PAGE + LC-MS/MS with Novor + PEAKS de novo sequencing and MS-BLAST similarity search to characterize the venom proteome of the hump-nosed pit viper (Western Ghats).
  • Ruby ant venom decapeptide (2019): Combined Edman degradation and de novo peptide sequencing to isolate and characterize U-MYRTX-MRArub1, a novel insecticidal decapeptide from Myrmica rubra ant venom.
  • Malabar pit viper venomics (2020): Venomics workflow combining SDS-PAGE and ion-exchange pre-fractionation with LC-MS/MS + Novor and PEAKS de novo sequencing to identify 97 proteins (including 18 exclusive to de novo) from Trimeresurus malabaricus venom, and evaluate antivenom cross-reactivity.
  • Anatolian meadow viper top-down ISD venomics (2020): Extended top-down venomics workflow using in-source decay (ISD) with 1,5-diaminonaphthalene reducing matrix to enable disulfide-bond counting and de novo sequencing-based identification of high-molecular-weight venom constituents, applied to the newly described Vipera anatolica senliki.
  • Naja naja venomics (2022): Venomics + antivenomics workflow using SDS-PAGE, RP-HPLC and Q-TOF LC-MS/MS with PEAKS + Novor de novo sequencing to identify 115 proteins across 17 venom protein families in Indian cobra venom from the Western Ghats, and benchmark polyvalent-antivenom recognition.
  • Daboia siamensis multi-omics venomics (2022): Multi-omics venomics of Russell’s viper (Daboia siamensis, Thai specimens): 10x-linked-read + short-read genome assembly and venom-gland transcriptomics feed a MAKER-annotated CDS database, which is searched with PEAKS Studio (database) plus SMSNet (deep-learning de novo) to identify 1,662 venom proteins including previously unreported hyaluronidase-1, phospholipase B and waprin.
  • Bothrops moojeni venom protease de novo identification (2022): Reviews the state of identifying wholly unknown proteins by mass spectrometry and demonstrates it on a snake venom serine protease from Bothrops moojeni, where de novo sequence tags such as D[K/Q]D[I/L]VDD[K/Q] made the identification.
  • Snake venomics quantification review (2023): Calvete-lab review of mass-spectrometry-based quantification of snake venom proteomes for non-model species: label-free strategies, absolute quantification via ICP-MS, hybrid elemental/molecular MS setups. Discusses manual de novo interpretation as an established workflow for non-model venomics.
  • Scorpion venom short peptides (2024): LC-HRMS with de novo sequencing of short (2-12 aa) scorpion venom peptides: 156 sequences identified, revealing N- and C-terminal modifications including the previously unreported N-benzoyl modification.
  • Conus regius conopeptidome (2025): Reversed-phase LC + Q-TOF MS/MS with Peaks Studio v7 de novo sequencing to identify 520 conopeptides from the vermivorous cone snail Conus regius, spanning 13 conotoxin gene superfamilies and eight disulfide-poor peptide classes: the first molluscan entry in the venomics lane.

Papers (13)

Sequencing tools these papers used

MS BLAST, Manual MS/MS de novo interpretation, Novor, PEAKS, SMSNet

Authors (85)

Alica Klaus, Amit Pal, Andreas Vilcinskas, Anthony J. Saviola, Athira Radhamony Murali, Ayse Nalbantsoy, Bayram Göçmen, Benjamin-Florian Hempel, Bipin Gopalakrishnan Nair, Bruno Lomonte, Cangman Zhang, Cheng Zhang, Daniel C. Pimenta, Dileepkumar Raveendran, Emídio Beraldo-Neto, Fabiana V. Campos, Francisco Calderón Celis, Helena B. Fiorotti, Hongyue Ma, Huixia Zhang, Ivy Rose Sebastian, Jia Long, Jianfeng Qin, Jianfeng Sun, Jie Dai, Jinao Duan, Jing Zhou, Jingguang Lu, Johannes A. Eble, John Heep, Jorge Ruiz Encinar, Juan J. Calvete, Kenneth Hodge, Khin Than Yee, Lawan Chanhome, Ling Zeng, Luis Alberto Ponce-Soto, Maik Damm, Marisa Skaljac, Mark A. Knepper, Maximilian Seip, Mei Zhou, Mert Karış, Mingrong Yang, Mrinalini, Muralidharan Vanuopadath, Naixuan Cai, Narongsak Chaiyabutr, Nayana Sudish, Nidhi Dalpatraj Jain, Nithin Sajeev, Nithya Kangosseri, Orawan Khow, Peter Roepstorff, Ping Chen, Poorichaya Somparn, Qinan Wu, R. Manjunatha Kini, Roderich D. Süssmuth, Ruoxian Xv, Sanu Korumadathil Shaji, Sergio Marangoni, Simone König, Sira Sriswasdi, Songping Liang, Sudarslal Sadasivan Nair, Suely G. Figueiredo, Sunchai Payungporn, Thalita Rocha, Thammakorn Saethang, Thiago Verano-Braga, Tianbao Chen, Tobias Kessel, Trairak Pisitkun, Victor Corasolla Carregari, Visith Sitprija, Wei Zhang (Macau), Wenlong Zhang, Wolfgang M. J. Obermann, Xianchun Wang, Xinping Xi, Yiguo Huo, Ying Wang, Zhihong Jiang, Zhonghua Liu

Where the work happened

Brazil, China, Costa Rica, Denmark, Germany, India, Myanmar, Singapore, Spain, Thailand, Turkey, UK, USA

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