cptac Phosphoproteome searching

[XiaofengxBjmu]

If I want to search CPTAC Phosphoproteome data with TMT11 and Thermo Orbitrap Fusion Lumos, why the param of comet are comet.params.high-low (As written later). But I saw some paper with 0.05Da fragment mass tol. And what is the relationship between these two parameters, 0.05Da and 1.0005 fragment_bin_tol.

fragment_bin_tol = 1.0005 # binning to use on fragment ions
fragment_bin_offset = 0.4 # offset position to start the binning (0.0 to 1.0)
theoretical_fragment_ions = 1 # 0=use flanking peaks, 1=M peak only
use_A_ions = 0
use_B_ions = 1
use_C_ions = 0
use_X_ions = 0
use_Y_ions = 1
use_Z_ions = 0
use_Z1_ions = 0
use_NL_ions = 0 # 0=no, 1=yes to consider NH3/H2O neutral loss peaks

Thank you very much in advance.

[prvst]

Hi @XiaofengxBjmu, you should redirect those questions to the Comet maintainers, we just distribute their program within our tools. You can reach out to them here