Constructing an MSP database for MS2 fragmentation October 13, 2020, 05:18:03 PM Dear all, I am in the process of constructing an MSP database for MS2 fragmentation of common secondary metabolites produced by marine algae. I have been using CFM-ID to generate fragmentation predictions. I am interested in identifying hydrogen, sodium, and ammonium adducts for these compounds. However, I am running into some issues as I proceed with data analysis from seawater samples, so I would like to inquire if my setup for these adducts in my database may be incorrect. Here is an example: NAME: Pectenotoxin_11_NaPRECURSORMZ: 897.460PRECURSORTYPE: [M+H+Na]+FORMULA: C47H70O15INCHIKEY: ASJMRRUHURWTNM-YOPFHQOQSA-NSMILES: CC1CCOC(C1O)(C2C(C3C(O2)C=CC(=CC(CC4(CCC(O4)C56CCC(O5)(CC(O6)C7C(=O)CC(O7)(C(C8CCC9(O8)CCCC(O9)C(C(=O)O3)C)O)C)C)C)C)C)O)OIONMODE: PositiveNum Peaks: 5241.0022 551.0229 853.0386 755.0542 1857.0699 1259.0855 1071.0491 1383.0491 2485.0648 987.0804 7101.0597 4103.0754 4127.039 5131.0703 4133.0859 11191.0914 5683.379 9699.3739 6701.3895 8713.3895 7725.3895 14729.3845 4731.4001 2743.4001 7745.4158 4843.4525 5857.4682 12859.4474 6875.4787 4641.0386 543.0178 843.0542 745.0335 18173.0808 5715.4052 5727.3688 6727.4052 8801.4056 2839.4576 7845.4682 4847.4838 539.0229 557.0335 959.0491 469.0335 569.0699 473.0648 581.0335 9115.0754 4129.0546 2711.3739 7729.4208 5Thank you, Tatiana Quote Selected
Re: Constructing an MSP database for MS2 fragmentation Reply #1 – October 30, 2020, 11:15:04 AM Hi Tatiana,you should be changed to [M+Na]+ for the sodium adduct information.According to the SMILES code, the exact mass is 874.4714.Because the precursor m/z is 897.46, it can be expected as [M+Na]+ because the exact mass of Na+ is 22.9892.Thanks,Hiroshi Quote Selected