nf-core/diaproteomics

Input sample sheet (containing path and meta data of raw or mzML files)

Input sample sheet of spectral libraries (tsv, pqp, TraML)

Path to internal retention time standard sample sheet (tsv, pqp, TraML)

The output directory where the results will be saved.

Email address for completion summary.

Set this flag if the spectral library should be generated using EasyPQP from provided DDA data - identification search results and corresponding raw data.

Input sample sheet to use for library generation eg. DDA raw data (mzML) and DDA identification data (pepXML, mzid, idXML)

PSM fdr threshold to align peptide ids with reference run.

Minimum number of transitions for assay

Maximum number of transitions for assay

Method for generating decoys

Set this flag if using a spectral library that already includes decoy sequences and therefor skip assay and decoy generation.

Path to unimod file needs to be provided

Set this flag if you only want to generate spectral libraries from DDA data

Set this flag if pseudo internal retention time standards should be generated using EasyPQP from provided DDA data - identification search results and corresponding raw data.

Number of pseudo irts selected from dda identifications based on the best q-value

Set this flag if pseudo irts should be selected from the 1st and 4th RT quantile only

Set this flag if the libraries defined in the input or by generation should be merged according to the BatchID

Set this flag if pairwise RT alignment should be applied to libraries when merging.

Minimum number of peptides to compute RT alignment during pairwise merging of libraries

Mass tolerance for transition extraction (ppm)

Unit for mz window

Mass tolerance for precursor transition extraction (ppm)

Unit for mz window

RT window for transition extraction (seconds)

Minimal random mean squared error for irt RT alignment

Number of bins defined for the RT Normalization

Number of bins that have to be covered for the RT Normalization

Method for irt RT alignment for example

Force the analysis of the OpenSwathWorkflow despite severe warnings

Whether to use ms1 information for scoring and extraction

Minimal distance to the upper edge of a Swath window to still consider a precursor, in Thomson

Set mode whether to work in memory or to store data as cache first

Machine learning classifier used for pyprophet target / decoy separation

MS Level of pyprophet FDR calculation

Abstraction level of pyrophet FDR calculation

Threshold for pyprophet FDR filtering on peakgroup abstraction level

Threshold for pyprophet FDR filtering on peptide abstraction level

Threshold for pyprophet FDR filtering on protein abstraction level

Start for pyprophet non-parametric pi0 estimation

End for pyprophet non-parametric pi0 estimation

Steps for pyprophet non-parametric pi0 estimation

DIAlignR global alignment FDR threshold: After the chromatogram alignment all peaks should still satisfy the global alignment FDR threshold.

DIAlignR analyte FDR threshold: Before the chromatogram alignment only peaks satisfying this threshold will be matched across runs.

DIAlignR unalignment FDR threshold: XICs below this threshold will be considered valid without any alignment.

DIAlignR alignment FDR threshold: After the chromatogram alignment aligned peaks should satisfy this threshold.

DIAlignR query FDR threshold: During the chromatogram alignment only peaks satisfying this maximum FDR threshold will be considered as potential matches.

DIAlignR XICfilter parameter

Whether DIAlignR should be executed using multithreading (may cause errors)

Set this flag if statistical normalization and visualizations should be generated using MSstats

Set this flag if output plots should be generated.

Optional mzTab export (Warning: the mzTab format is not yet well supported for DIA)