Comparative Snake Venom Analysis for Facilitating Wildlife Forensics: A Pilot Study

Table 1

Details of various machine and experiment parameters of LC-MS/MS analysis of snake venoms.

General reverse-phase nano-liquid chromatography parameters	General Mass spectrometer parameters	Database searching parameters
Instrument name: Thermo Scientific Easy-nLC 1200	Instrument name: Thermo Scientific Q Exactive Orbitrap	Software used: Proteome Discoverer 2.2
(i) Amount of peptide loaded on column: ∼3 µg; (ii) Analytical column name: PepMap RSLC C18 2µm × 50 cm (Thermo scientific); (iii) Column temperature: 40^0 C	General setting: (i) Run time: 0 to 140 min; (ii) Polarity: Positive; (iii) Default charge state: 2; MS (MS1) setting: (i) Microscan: 1; (ii) Resolution: 70000; (iii) AGC (Automatic gain control) 3e^6; (iv) Maximum IT (ion transfer) time: 50 ms; (v) No. of scan ranges: 1; (vi) Scan ranges: 350 to 1700m/z; (vii) Spectrum obtained was in profile mode; MS MS (MS2) setting: (i) Microscan: 1; (ii)Resolution: 17500; (iii)AGC (Automatic gain control) 2e^5; (iv)Maximum IT (ion transfer) 100 ms; (v) Loop count: 15 (top 15 masses will be fragmented one by one); (vi) Maximum number of precursor to be plexed in single event: 1; (vii) Isolation window: 1.2 m/z; (viii) Isolation offset: 0.0 m/z; (ix) Fixed first mass: 100 m/z; (x) Normalized collision energy: 27; (xi) Data dependent settings; (xii) Minimum AGC target: 1.20e^2; (xiii) Charge exclusion: unassigned, 1, 7, 8, >8; (xiv) Dynamic exclusion time: 50.0 S	Database of SERPENTES was directly downloaded from http://www.uniprot.org in fasta format.; (i) Maximum allowed missed cleavage: 2; (ii) Minimum peptide length for search: 2; (iii) Maximum peptide length: 144; (iv) Precursor mass tolerance: 10 ppm; (v) Fragment mass tolerance: 0.02 Da; (vi) Dynamic modification: Oxidation of Methionine and Acetylation at N terminus; (vii) Static modification: Carbamidomethylation; (viii) Target FDR (false discovery rate): 0.01 (for decoy database search); (ix) Validation was based on q value.