| ion_mode |
|
MS ion mode | "positive" or "negative" |
| ms_type |
|
type of MS | "orbitrap" "qtof" "tripletof" or "others" |
| is_centroid |
|
whether the raw data is centroid data | "yes" or "no" |
| mz_lower_limit |
|
lower limit of m/z in Da |
| mz_upper_limit |
|
upper limit of m/z in Da |
| rt_lower_limit |
|
lower limit of retention time in minutes |
| rt_upper_limit |
|
upper limit of retention time in minutes |
| ms1_abs_int_tol |
|
absolute intensity threshold for MS1 | recommend 30000 for
Orbitrap and 1000 for QTOF
|
| ms2_abs_int_tol |
|
absolute intensity threshold for MS2 | recommend 10000 for
Orbitrap and 500 for QTOF
|
| mz_tol_ms1 |
|
m/z tolerance for MS1 | default is 0.01 |
| mz_tol_ms2 |
|
m/z tolerance for MS2 | default is 0.015 |
| scan_scan_cor_tol |
|
scan-to-scan correlation tolerance for feature grouping | default
is 0.7
|
| mz_tol_alignment |
|
m/z tolerance for alignment | default is 0.01 |
| rt_tol_alignment |
|
RT tolerance for alignment | default is 0.2 |
| correct_rt |
|
whether to perform RT correction |
| merge_features |
|
whether to clean feature table by merging features with almost the
same m/z and RT
|
| ms2_library_path |
|
path to the MS2 library (.msp or .pickle) |
| ms2_sim_tol |
|
MS2 similarity tolerance |
| consider_rt |
|
whether to consider RT information for MS2 matching | "yes" or
"no"
|
| rt_tol_annotation |
|
RT tolerance for MS2 annotation | default is 0.2 minutes |
| fuzzy_search |
|
whether to perform fuzzy search |
| sample_normalization |
|
whether to normalize the data based on total sample
amount/concentration
|
| signal_normalization |
|
whether to run feature-wised normalization to correct systematic
signal drift
|
| run_statistics |
|
whether to perform statistical analysis |
| plot_bpc |
|
whether to plot base peak chromatograms |
| plot_ms2 |
|
whether to plot mirror plots for MS2 matching |
| plot_normalization |
|
whether to the normalization results |
| quant_method |
|
value for quantification and output | "peak_height" "peak_area" or
"top_average"
|