PrecursorIonSelector
Web Documentation for PrecursorIonSelector
Version of the tool that generated this parameters file.
number of precursors to be selected
The preprocessed db is loaded from file, not calculated.
The preprocessed db is stored.
Simulate the whole LC-MS/MS run.
File containing the results of the simulation run
SVM Model for RTPredict
SVM Model for PTPredict
LP solver type
the modifications i.e. Carboxymethyl (C)
Name of log file (created only when specified)
Sets the debug level
Sets the number of threads allowed to be used by the TOPP tool
Disables progress logging to command line
Overwrite tool specific checks.
Enables the test mode (needed for internal use only)
Strategy for precursor ion selection.
Maximal number of iterations.
Maximal number of precursors per rt bin.
Maximal number of precursors per iteration.
Minimal peptide probability.
If true, precursors are selected sequentially with respect to their RT.
Minimal protein probability for a protein to be considered in the ILP
Minimal protein probability for a protein to be considered identified.
Minimal pt weight of a precursor
Minimal mz to be considered in protein based LP formulation.
Minimal mz to be considered in protein based LP formulation.
Minimal predicted peptide probability of a precursor
Minimal rt weight of a precursor
Use peptide rule instead of minimal protein id probability
If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id
If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified
combined ilp: weight for z_i
combined ilp: weight for x_j,s*int_j,s
combined ilp: weight for -x_j,s*w_j,s
flag if detectability * rt_weight shall be scaled to cover all [0,1]
Flag indicating if intensities shall be scaled to be in [0,1]. This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1.
The maximal number of precursors per feature.
Precursor mass tolerance which is used to query the peptide database for peptides
Precursor mass tolerance unit.
Path where the preprocessed database should be stored
Path where the predicted rts of the preprocessed database should be stored
Path where the predicted rts of the preprocessed database should be stored
Number of peptides for that the pt and rt are parallely predicted.
Number of allowed missed cleavages.
Taxonomy
Absolute path to tmp data directory used to store files needed for rt and dt prediction.
Flag if peptide sequences should be stored.
Minimal RT in the experiment (in seconds)
Maximal RT in the experiment (in seconds)
Time between two consecutive spectra (in seconds)
mean of the gauss curve
std of the gauss curve