ProteoMaker Simulator

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Run statistical tests on results

Overwrite existing files

Calculate benchmarking metrics

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Select Simulation Stage

Table

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Parameter Groups

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Download YAML File

Experimental Design

Number of conditions.

Number of replicates.

Input Data

Path to input FASTA file.

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Path to input protein list (optional).

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Ground Truth Data

Fraction of expressed proteins from fasta file.

Fraction of proteins selected to be modified (0 for none, 1 for all).

Factor for generating more that many modified proteoforms per selected protein.

Poisson parameter for multiply modified proteins, scaled to the number of possible PTM sites.

Fraction of modifiable proteins without non-modified forms.

Post-Translational Modifications

Select PTM

Fraction of this PTMs within all PTMs, use '1 for equal contributions. Will be normalized to a total of one.

Distribution PTMs over amino acids, will be normalized to a total sum of 1

Current PTMs

Proteoform Quantities

Noise level of quantitative values (standard deviation).

Fraction of differentially regulated proteoforms.

Maximum amplitude of difference for differentially regulated proteoforms (log2 scale).

Custom set of regulated proteoforms (optional). Number of regulated proteoforms

Custom set of regulated proteoforms (optional). Fold change of regulation.

Mean for absolute quantification.

Standard deviation for absolute quantification.

Quantile threshold for removing quantitative values.

Enzymatic Digestion

Enzyme used for digestion (e.g., trypsin).

Proportion of peptides with missed cleavages.

Maximum number of missed cleavages per peptide.

Minimum peptide length.

Maximum peptide length.

Fraction of least abundant peptides to remove.

Sample Preparation

Post-translational modification (PTM) that will be enriched.

Fraction loss of peptides during enrichment.

Efficiency of enrichment for modified peptides (fraction).

Quantitative difference (means on log-scale) between enriched and non-enriched peptifdes in enriched samples.

Noise due to enrichment protocol.

Fraction loss of modified peptides in non-enriched samples during sample preparation.

MS Run

Keeping the given percentage of peptides according to their predicted detectibility from PeptideRanger predictions (trained on ProteomicsDB).

Fraction of detected values (replicate/condition).

Weights for intensity-dependence of non-detection.

Noise due to the MS instrument.

MS Search

Fraction of wrong identifications.

Fraction of wrong localizations.

MS Search Results Filter

Maximum number of NA values per peptide allowed.

Protein Summarization

Method for summarizing to proteins (e.g., sum.top3, medpolish).

Minimum number of unique peptides available.

Statistical Testing

Whether the statistical testing is paired or unpaired.