The data analysis was performed using MetaMorpheus version 1.0.1, available at https://github.com/smith-chem-wisc/MetaMorpheus.
The following crosslink discovery were used: crosslinker name = DSSO_KSTY; crosslinker type = True; crosslinker mass = 158.0038; crosslinker modification site(s) = KSTY; protease = trypsin; maximum missed cleavages = 3; minimum peptide length = 5; maximum peptide length = 60; initiator methionine behavior = Variable; max modification isoforms = 1024; fixed modifications = Carbamidomethyl on C, Carbamidomethyl on U; variable modifications = Oxidation on M, DSSO_alkene_K on K, DSSO_alkene_Nt on X, DSSO_alkene_S on S, DSSO_alkene_T on T, DSSO_alkene_Y on Y, DSSO_hydro_K on K, DSSO_hydro_Nt on X, DSSO_hydro_S on S, DSSO_hydro_T on T, DSSO_hydro_Y on Y, DSSO_hydrotris_K on K, DSSO_hydrotris_Nt on X, DSSO_hydrotris_S on S, DSSO_hydrotris_T on T, DSSO_hydrotris_Y on Y, DSSO_loop_K on K, DSSO_loop_Nt on X, DSSO_loop_S on S, DSSO_loop_T on T, DSSO_loop_Y on Y, DSSO_thiol_K on K, DSSO_thiol_Nt on X, DSSO_thiol_S on S, DSSO_thiol_T on T, DSSO_thiol_Y on Y; parent mass tolerance(s) = ±10.0000 PPM; product mass tolerance = ±20.0000 PPM; The combined search database contained 4 total entries including 0 contaminant sequences. Data files were processed on a computer running Microsoft Windows 10.0.17763 with a 64-bit Intel(R) Xeon(R) Gold 6238 CPU @ 2.10GHz processor with 44 threads and 512GB installed RAM. 
The total time to perform the XLSearch task on 4 spectra file(s) was 10.92 minutes.

Published works using MetaMorpheus software are encouraged to cite: Solntsev, S. K.; Shortreed, M. R.; Frey, B. L.; Smith, L. M. Enhanced Global Post-translational Modification Discovery with MetaMorpheus. Journal of Proteome Research. 2018, 17 (5), 1844-1851.

Spectra files: 
	Z:\FPL_users\2023\Lumos\Zheng Wint XLMS\20231215_WP_eD4FL\20231215_Lumos_ZS_WP_eD4FL_S48A_ctrl.raw
	Z:\FPL_users\2023\Lumos\Zheng Wint XLMS\20231215_WP_eD4FL\20231215_Lumos_ZS_WP_eD4FL_S48A_dsso_T1.raw
	Z:\FPL_users\2023\Lumos\Zheng Wint XLMS\20231215_WP_eD4FL\20231215_Lumos_ZS_WP_eD4FL_S48A_dsso_T2.raw
	Z:\FPL_users\2023\Lumos\Zheng Wint XLMS\20231215_WP_eD4FL\20231215_Lumos_ZS_WP_eD4FL_S48A_dsso_T3.raw
Databases:
	Z:\FPL_users\2023\Lumos\Zheng Wint XLMS\20231215_WP_eD4FL\eD4FL_S48A.fasta Downloaded on: 01/11/2024 10:17:52