PrecursorIonSelector

Options

version

Version of the tool that generated this parameters file.

num_precursors

number of precursors to be selected

load_preprocessing

The preprocessed db is loaded from file, not calculated.

store_preprocessing

The preprocessed db is stored.

simulation

Simulate the whole LC-MS/MS run.

solver

LP solver type

fixed_modifications

the modifications i.e. Carboxymethyl (C)

log

Name of log file (created only when specified)

debug

Sets the debug level

threads

Sets the number of threads allowed to be used by the TOPP tool

no_progress

Disables progress logging to command line

force

Overrides tool-specific checks

test

Enables the test mode (needed for internal use only)

type

Strategy for precursor ion selection.

max_iteration

Maximal number of iterations.

rt_bin_capacity

Maximal number of precursors per rt bin.

step_size

Maximal number of precursors per iteration.

peptide_min_prob

Minimal peptide probability.

sequential_spectrum_order

If true, precursors are selected sequentially with respect to their RT.

min_protein_probability

Minimal protein probability for a protein to be considered in the ILP

min_protein_id_probability

Minimal protein probability for a protein to be considered identified.

min_pt_weight

Minimal pt weight of a precursor

min_mz

Minimal mz to be considered in protein based LP formulation.

max_mz

Minimal mz to be considered in protein based LP formulation.

min_pred_pep_prob

Minimal predicted peptide probability of a precursor

min_rt_weight

Minimal rt weight of a precursor

use_peptide_rule

Use peptide rule instead of minimal protein id probability

min_peptide_ids

If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id

min_peptide_probability

If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified

k1

combined ilp: weight for z_i

k2

combined ilp: weight for x_j,s*int_j,s

k3

combined ilp: weight for -x_j,s*w_j,s

scale_matching_probs

flag if detectability * rt_weight shall be scaled to cover all [0,1]

no_intensity_normalization

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.

max_number_precursors_per_feature

The maximal number of precursors per feature.

precursor_mass_tolerance

Precursor mass tolerance which is used to query the peptide database for peptides

precursor_mass_tolerance_unit

Precursor mass tolerance unit.

preprocessed_db_path

Path where the preprocessed database should be stored

preprocessed_db_pred_rt_path

Path where the predicted rts of the preprocessed database should be stored

preprocessed_db_pred_dt_path

Path where the predicted rts of the preprocessed database should be stored

max_peptides_per_run

Number of peptides for that the pt and rt are parallelly predicted.

missed_cleavages

Number of allowed missed cleavages.

taxonomy

Taxonomy

tmp_dir

Absolute path to tmp data directory used to store files needed for rt and dt prediction.

store_peptide_sequences

Flag if peptide sequences should be stored.

min_rt

Minimal RT in the experiment (in seconds)

max_rt

Maximal RT in the experiment (in seconds)

rt_step_size

Time between two consecutive spectra (in seconds)

gauss_mean

mean of the gauss curve

gauss_sigma

std of the gauss curve

Views

PrecursorIonSelector Std Output

The text sent to standard out during the execution of PrecursorIonSelector.

PrecursorIonSelector Error Output

The text sent to standard error during the execution of PrecursorIonSelector. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

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