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Parameter: MS_data_file

Overview

Name of the data file to be analyzed. It is recommended to include the path in the name of the file. mzML or Thermo RAW formats are recommended over mzXML, as they contain useful metadata that aid in the spectral analysis.

Syntax

[Text]

Supported File Formats

  • mzXML
  • mzML
  • Thermo RAW (on Windows with vendor drivers installed)

Example

MS_data_file = my_data.mzML
Overview
General Info Sample Configuration File
Data I/O
database export_pepXML export_percolator MS_data_file percolator_version results_path split_pepxml
Data Descriptors
enrichment instrument MS1_centroid MS1_resolution MS2_centroid MS2_resolution
Cross-links
cross_link mono_link predefined_crosslink xl_cleavage_product_mass
Modifications
aa_mass diff_mods_on_xl fixed_modification fixed_modification_protC fixed_modification_protN max_mods_per_peptide modification modification_protC modification_protN mono_links_on_xl
Scoring Algorithm
fragment_bin_offset fragment_bin_size ion_series_A ion_series_B ion_series_C ion_series_X ion_series_Y ion_series_Z
Analysis
decoy_filter diagnostic e_value_depth enzyme isotope_error max_miscleavages max_peptide_mass max_spectrum_peaks min_peptide_mass min_peptide_score min_spectrum_peaks ppm_tolerance_pre precursor_refinement prefer_precursor_pred spectrum_processing threads top_count truncate_prot_names
Deprecated Parameters
output_file percolator_file search_dimers turbo_button use_comet_xcorr

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