Epifany

Options

version

Version of the tool that generated this parameters file.

protein_fdr

Additionally calculate the target-decoy FDR on protein-level based on the posteriors

conservative_fdr

Use (D+1)/(T) instead of (D+1)/(T+D) for reporting protein FDRs.

picked_fdr

Use picked protein FDRs.

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.

greedy_group_resolution

Post-process inference output with greedy resolution of shared peptides based on the parent protein probabilities. Also adds the resolved ambiguity groups to output.

min_psms_extreme_probability

Set PSMs with probability lower than this to this minimum probability.

max_psms_extreme_probability

Set PSMs with probability higher than this to this maximum probability.

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)

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?

update_PSM_probabilities

(Experimental:) Update PSM probabilities with their posteriors under consideration of the protein probabilities.

user_defined_priors

(Experimental:) Uses the current protein scores as user-defined priors.

annotate_group_probabilities

Annotates group probabilities for indistinguishable protein groups (indistinguishable by experimentally observed PSMs).

use_ids_outside_features

(Only consensusXML) Also use IDs without associated features for inference?

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.

Views

Epifany Std Output

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

Epifany Error Output

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

Workflows

• Identification_quantification_with_inference_isobaric_epifany_MSstatsTMTOpenMS
• Identification_quantification_with_inference_isobaric_epifany_MSstatsTMTKNIME Hub
• Phosphoproteomics_IDKNIME Hub
• Phosphoproteomics_IDOpenMS

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