Repeated Enhancing with Featured Ion-Guided Stoichiometry (RE-FIGS) is a complete and compact solution on DI-SPA data for more confident identifications and corresponding label free quantifications.

The bootstrap aggregation linear discriminant analysis based identification.

• mzML_file: the mzml file path
• SSM_file: the spectrum spectrum match results file (csodiaq csv format file before FDR filtering)
• lib_file: the spectral library path
• start_cycle: the cycle No. starts from
• end_cycle: the cycle No. ends with
• good_shared_limit: the threshold to select good target.
• good_cos_sim_limit: the threshold to select good target. range(0,1)
• good_sqrt_cos_sim_limit: the threshold to select good target. range(0,1)
• good_count_within_cycle_limit: the threshold to select good target.
• tol: fragment mass error(tolerance) in ppm.
• scans_per_cycle: the scan number in each cycle.
• seed: the seed to randomly choose decoy.

label free quantification on DI-SPA data.

• mzML_file:the mzml file path
• SSM_file: the final identification results file
• lib_file: the spectral library path
• topN: keep topN peaks in spectral library.
• tol: fragment mass error(tolerance) in ppm.