IsobaricWorkflow

Options

version

Version of the tool that generated this parameters file.

type

Isobaric Quantitation method used in the experiment.

calculate_id_purity

Calculate the purity of the precursor ion based on the MS1 spectrum. Only used for MS3, otherwise it is the same as the quant. precursor purity.

psm_score

The score which should be reached by a peptide hit to be kept. (use 'NAN' to disable this filter)

protein_score

The score which should be reached by a protein hit to be kept. All proteins are filtered based on their singleton scores irrespective of grouping. Use in combination with 'delete_unreferenced_peptide_hits' to remove affected peptides. (use 'NAN' to disable this filter)

delete_unreferenced_peptide_hits

Peptides not referenced by any protein are deleted in the IDs.

inference_method

Methods used for protein inference

picked_fdr

Use a picked protein FDR

picked_decoy_string

If using picked protein FDRs, which decoy string was used? Leave blank for auto-detection.

picked_decoy_prefix

If using picked protein FDRs, was the decoy string a prefix or suffix? Ignored during auto-detection.

FDR_type

Sub-protein FDR level. PSM, PSM+peptide (best PSM q-value).

proteinFDR

Protein FDR threshold (0.05=5%).

psmFDR

FDR threshold for sub-protein level (e.g. 0.05=5%).

protein_quantification

Quantify proteins based on: unique_peptides = use peptides mapping to single proteins or a group of indistinguishable proteins(according to the set of experimentally identified peptides). strictly_unique_peptides = use peptides mapping to a unique single protein only. shared_peptides = use shared peptides only for its best group (by inference score)

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)

method

- top - quantify based on three most abundant peptides (number can be changed in 'top'). - iBAQ (intensity based absolute quantification), calculate the sum of all peptide peak intensities divided by the number of theoretically observable tryptic peptides (https://rdcu.be/cND1J). Warning: only consensusXML or featureXML input is allowed!

best_charge_and_fraction

Distinguish between fraction and charge states of a peptide. For peptides, abundances will be reported separately for each fraction and charge; for proteins, abundances will be computed based only on the most prevalent charge observed of each peptide (over all fractions). By default, abundances are summed over all charge states.

N

Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)

aggregate

Aggregation method used to compute protein abundances from peptide abundances

include_all

Include results for proteins with fewer proteotypic peptides than indicated by 'N' (no effect if 'N' is 0 or 1)

normalize

Scale peptide abundances so that medians of all samples are equal

fix_peptides

Use the same peptides for protein quantification across all samples. With 'N 0',all peptides that occur in every sample are considered. Otherwise ('N'), the N peptides that occur in the most samples (independently of each other) are selected, breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!).

min_peptides_per_protein

Minimal number of peptides needed for a protein identification. If set to zero, unmatched proteins get a score of -Infinity. If bigger than zero, proteins with less peptides are filtered and evidences removed from the PSMs. PSMs that do not reference any proteins anymore are removed but the spectrum info is kept.

score_aggregation_method

How to aggregate scores of peptides matching to the same protein?

treat_charge_variants_separately

If this is true, different charge variants of the same peptide sequence count as individual evidences.

treat_modification_variants_separately

If this is true, different modification variants of the same peptide sequence count as individual evidences.

use_shared_peptides

If this is true, shared peptides are used as evidences. Note: shared_peptides are not deleted and potentially resolved in postprocessing as well.

skip_count_annotation

If this is set, peptide counts won't be annotated at the proteins.

score_type

PSM score type to use for inference. (default: empty = main score)

psm_probability_cutoff

Remove PSMs with probabilities less than this cutoff

top_PSMs

Consider only top X PSMs per spectrum. 0 considers all.

keep_best_PSM_only

Epifany uses the best PSM per peptide for inference. Discard the rest (true) or keepe.g. for quantification/reporting?

prot_prior

Protein prior probability ('gamma' parameter). Negative values enable grid search for this param.

pep_emission

Peptide emission probability ('alpha' parameter). Negative values enable grid search for this param.

pep_spurious_emission

Spurious peptide identification probability ('beta' parameter). Usually much smaller than emission from proteins. Negative values enable grid search for this param.

pep_prior

Peptide prior probability (experimental, should be covered by combinations of the other params).

regularize

Regularize the number of proteins that produce a peptide together (experimental, should be activated when using higher p-norms).

extended_model

Uses information from different peptidoforms also across runs (automatically activated if an experimental design is given!)

scheduling_type

(Not used yet) How to pick the next message: priority = based on difference to last message (higher = more important). fifo = first in first out. subtree = message passing follows a random spanning tree in each iteration

convergence_threshold

Initial threshold under which MSE difference a message is considered to be converged.

dampening_lambda

Initial value for how strongly should messages be updated in each step. 0 = new message overwrites old completely (no dampening; only recommended for trees),0.5 = equal contribution of old and new message (stay below that),In-between it will be a convex combination of both. Prevents oscillations but hinders convergence.

max_nr_iterations

(Usually auto-determined by estimated but you can set a hard limit here). If not all messages converge, how many iterations should be done at max per connected component?

p_norm_inference

P-norm used for marginalization of multidimensional factors. 1 == sum-product inference (all configurations vote equally) (default),<= 0 == infinity = max-product inference (only best configurations propagate)The higher the value the more important high probability configurations get.

aucweight

How important is target decoy AUC vs calibration of the posteriors? 0 = maximize calibration only, 1 = maximize AUC only, between = convex combination.

conservative_fdr

Use (D+1)/(T) instead of (D+1)/(T+D) for parameter estimation.

regularized_fdr

Use a regularized FDR for proteins without unique peptides.

select_activation

Operate only on MSn scans where any of its precursors features a certain activation method. Setting to "auto" uses HCD and HCID spectra. Set to empty string if you want to disable filtering.

reporter_mass_shift

Allowed shift (left to right) in Th from the expected position.

min_precursor_intensity

Minimum intensity of the precursor to be extracted. MS/MS scans having a precursor with a lower intensity will not be considered for quantitation.

keep_unannotated_precursor

Flag if precursor with missing intensity value or missing precursor spectrum should be included or not.

min_reporter_intensity

Minimum intensity of the individual reporter ions to be extracted.

discard_low_intensity_quantifications

Remove all reporter intensities if a single reporter is below the threshold given in 'min_reporter_intensity'.

min_precursor_purity

Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precursor.

precursor_isotope_deviation

Maximum allowed deviation (in ppm) between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precursor.

purity_interpolation

If set to true the algorithm will try to compute the purity as a time weighted linear combination of the precursor scan and the following scan. If set to false, only the precursor scan will be used.

channel_114_description

Description for the content of the 114 channel.

channel_115_description

Description for the content of the 115 channel.

channel_116_description

Description for the content of the 116 channel.

channel_117_description

Description for the content of the 117 channel.

reference_channel

Number of the reference channel (114-117).

correction_matrix

Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'

channel_113_description

Description for the content of the 113 channel.

channel_114_description

Description for the content of the 114 channel.

channel_115_description

Description for the content of the 115 channel.

channel_116_description

Description for the content of the 116 channel.

channel_117_description

Description for the content of the 117 channel.

channel_118_description

Description for the content of the 118 channel.

channel_119_description

Description for the content of the 119 channel.

channel_121_description

Description for the content of the 121 channel.

reference_channel

Number of the reference channel (113-121). Please note that 120 is not valid.

correction_matrix

Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'

isotope_correction

Enable isotope correction (highly recommended). Note that you need to provide a correct isotope correction matrix otherwise the tool will fail or produce invalid results.

normalization

Enable normalization of channel intensities with respect to the reference channel. The normalization is done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!

channel_126_description

Description for the content of the 126 channel.

channel_127N_description

Description for the content of the 127N channel.

channel_127C_description

Description for the content of the 127C channel.

channel_128N_description

Description for the content of the 128N channel.

channel_128C_description

Description for the content of the 128C channel.

channel_129N_description

Description for the content of the 129N channel.

channel_129C_description

Description for the content of the 129C channel.

channel_130N_description

Description for the content of the 130N channel.

channel_130C_description

Description for the content of the 130C channel.

channel_131_description

Description for the content of the 131 channel.

reference_channel

The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131).

correction_matrix

Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'

channel_126_description

Description for the content of the 126 channel.

channel_127N_description

Description for the content of the 127N channel.

channel_127C_description

Description for the content of the 127C channel.

channel_128N_description

Description for the content of the 128N channel.

channel_128C_description

Description for the content of the 128C channel.

channel_129N_description

Description for the content of the 129N channel.

channel_129C_description

Description for the content of the 129C channel.

channel_130N_description

Description for the content of the 130N channel.

channel_130C_description

Description for the content of the 130C channel.

channel_131N_description

Description for the content of the 131N channel.

channel_131C_description

Description for the content of the 131C channel.

reference_channel

The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C).

correction_matrix

Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'

channel_126_description

Description for the content of the 126 channel.

channel_127N_description

Description for the content of the 127N channel.

channel_127C_description

Description for the content of the 127C channel.

channel_128N_description

Description for the content of the 128N channel.

channel_128C_description

Description for the content of the 128C channel.

channel_129N_description

Description for the content of the 129N channel.

channel_129C_description

Description for the content of the 129C channel.

channel_130N_description

Description for the content of the 130N channel.

channel_130C_description

Description for the content of the 130C channel.

channel_131N_description

Description for the content of the 131N channel.

channel_131C_description

Description for the content of the 131C channel.

channel_132N_description

Description for the content of the 132N channel.

channel_132C_description

Description for the content of the 132C channel.

channel_133N_description

Description for the content of the 133N channel.

channel_133C_description

Description for the content of the 133C channel.

channel_134N_description

Description for the content of the 134N channel.

reference_channel

The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C, 132N, 132C, 133N, 133C, 134N).

correction_matrix

Correction matrix for isotope distributions in percent from the Thermo data sheet (see documentation); Please provide 16 entries (rows), separated by comma, where each entry contains 8 values in the following format: <-2C13>/<-N15-C13>/<-C13>/<-N15>/<+N15>/<+C13>/<+N15+C13>/<+2C13> e.g. one row may look like this: 'NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26'. You may use whitespaces at your leisure to ease reading.

channel_126_description

Description for the content of the 126 channel.

channel_127N_description

Description for the content of the 127N channel.

channel_127C_description

Description for the content of the 127C channel.

channel_128N_description

Description for the content of the 128N channel.

channel_128C_description

Description for the content of the 128C channel.

channel_129N_description

Description for the content of the 129N channel.

channel_129C_description

Description for the content of the 129C channel.

channel_130N_description

Description for the content of the 130N channel.

channel_130C_description

Description for the content of the 130C channel.

channel_131N_description

Description for the content of the 131N channel.

channel_131C_description

Description for the content of the 131C channel.

channel_132N_description

Description for the content of the 132N channel.

channel_132C_description

Description for the content of the 132C channel.

channel_133N_description

Description for the content of the 133N channel.

channel_133C_description

Description for the content of the 133C channel.

channel_134N_description

Description for the content of the 134N channel.

channel_134C_description

Description for the content of the 134C channel.

channel_135N_description

Description for the content of the 135N channel.

reference_channel

The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C, 132N, 132C, 133N, 133C, 134N, 134C, 135N).

correction_matrix

Correction matrix for isotope distributions in percent from the Thermo data sheet (see documentation); Please provide 18 entries (rows), separated by comma, where each entry contains 8 values in the following format: <-2C13>/<-N15-C13>/<-C13>/<-N15>/<+N15>/<+C13>/<+N15+C13>/<+2C13> e.g. one row may look like this: 'NA/0.00 / 0.82/0.65 / NA/8.13 / NA/0.26'. You may use whitespaces at your leisure to ease reading.

channel_126_description

Description for the content of the 126 channel.

channel_127_description

Description for the content of the 127 channel.

channel_128_description

Description for the content of the 128 channel.

channel_129_description

Description for the content of the 129 channel.

channel_130_description

Description for the content of the 130 channel.

channel_131_description

Description for the content of the 131 channel.

reference_channel

Number of the reference channel (126-131).

correction_matrix

Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>; e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'

Views

IsobaricWorkflow Std Output

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

IsobaricWorkflow Error Output

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

Workflows

• No workflows found

Links

• No links available

Developers