0 ×

PrecursorIonSelector

Generic Workflow Nodes for KNIME: OpenMS version 2.5.0.202002201806 by Freie Universitaet Berlin, Universitaet Tuebingen, and the OpenMS Team

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
Overwrite 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 parallely 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

Input Ports

Icon
Input feature map file (featureXML) [featureXML]
Icon
file containing results of identification [idXML]
Icon
Input profile data. [mzML,opt.]
Icon
db file [fasta,opt.]
Icon
SVM Model for RTPredict [txt,opt.]
Icon
SVM Model for PTPredict [txt,opt.]

Output Ports

Icon
modified feature map [featureXML]
Icon
feature map (featureXML) file with the selected precursors [featureXML]
Icon
File containing the results of the simulation run [txt]

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.)

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install OpenMS from the following update site:

KNIME 4.2
Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform.

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.