nf-core/mhcquant

Input raw / mzML files listed in a tsv file (see help for details)

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Email address for completion summary.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Input FASTA protein database

Set depending on whether variants should be translated to proteins and included into your fasta for database search.

Add this parameter when you want to skip the generation of the decoy database, the consequence is that it prevents the generation of variants and FDR refinement

Specify the MS levels for which the peak picking is applied (unless you use --run_centroidisation).

Include the flag when the specified ms level is not centroided (default=false).

Specify the minimum length of peptides to be considered after processing

Specify the maximum length of peptides to be considered after processing

Specify the fragment mass tolerance to be used for the comet database search.

Specify the precursor mass tolerance to be used for the comet database search.

Specify the fragment bin offset to be used for the comet database search.

Specify the maximum number of modifications that should be contained in a peptide sequence match.

Specify the number of hits that should be reported for each spectrum.

Specify the mass range that peptides should fulfill to be considered for peptide spectrum matching.

Specify the precursor charge range that peptides should fulfill to be considered for peptide spectrum matching.

Specify which fragmentation method was used in the MS acquisition

Set a maximum retention time shift for the linear rt alignment

Specify which fixed modifications should be applied to the database search

Specify which variable modifications should be applied to the database search

Include x ions into the peptide spectrum matching

Include z ions into the peptide spectrum matching

Include a ions into the peptide spectrum matching

Include c ions into the peptide spectrum matching

Include NL ions into the peptide spectrum matching

Include if you want to remove all peaks around precursor m/z

Size of Spectrum batch for Comet processing (Decrease/Increase depending on Memory Availability)

Specify a .tsv file containing the information about genomic variants (vcf files < v.4.2) for each sample.

Set this option to create documents that are created to perform the ion annotation

Comets theoretical_fragment_ions parameter: theoretical fragment ion peak representation, high-res: sum of intensities plus flanking bins, ion trap (low-res) ms/ms: sum of intensities of central M bin only

Default Comet params file. All parameters of this take precedence.

Clean up mzml files and remove artificial charge 0 peptides.

Specify the level at which the false discovery rate should be computed.

Specify the false discovery rate threshold at which peptide hits should be selected.

Set if MHCquant should be run in SubsetFDR mode

Affinity threshold (nM) used to define binders for PSM subset selection in the FDR refinement procedure

Specify percolator descriptor feature set

Use klammer retention time features for Percolator rescoring

Maximum subset for percolator training iterations

Use DeepLC retention time features for Percolator rescoring

Number of bins (peptides) used for DeepLC calibration. For each bin the best hit is used.

Specify the DeepLC calibration mode. rt_bin: bin peptides by RT, idx_bin: bin peptides by index, min_max: scale uncalibrated predictions to experimental RT range

Add absolute RT error to of experimental and predicted RT to the feature set

Add squared RT error to of experimental and predicted RT to the feature set

Add log RT error to of experimental and predicted RT to the feature set

Use MS2pip peak intensity prediction for Percolator rescoring

MS2pip model name defined (https://github.com/compomics/ms2pip#specialized-prediction-models)

Skip quantification and only yield peptide identifications

Compute FDR for the targeted approach

Specify a cut off probability value for quantification events as a filter

Specify a m/z window for matching between runs

Specify a rt window for matching between runs

Specify a rt mapping tolerance for mapping features between runs

Specify a peak width for feature extraction

Specify a minimum peak width for quantification

Specify a .tsv file containing the MHC alleles of your probes as well as their metadata such as SampleID.

Set flag depending on whether MHC class 1 binding predictions using the tool mhcflurry should be run.

Set flag depending on whether MHC class 2 binding predictions using the tool mhcnuggets should be run.

Specify genomic reference used for variant annotation

Specify style of tool used for variant annotation - currently supported

Set this option to not consider insertions and deletions for variant translation

Set this option to not consider frameshifts for variant translation

Set this option to not consider snps for variant translation

Custom MultiQC yaml file containing HTML including a methods description.