Spectral Processing

• min_peaks: Integer. Only process MS2 spectra with at least N peaks (default: 15).
• max_peaks: Integer. Take the top N most intense MS2 peaks to search (default: 150).
• min_matched_peaks: Integer. The minimum number of matched b+y ions required for scoring and reporting PSMs (default: 4).
• max_fragment_charge: Integer. The maximum fragment ion charge states to consider (default: null - use precursor z-1).

Sage does not perform any transformations on spectral intensity.

If deisotope is turned on, Sage will attempt to deisotope and deconvolute the charge state of fragment ions in an MS2 spectra. This can speed up searches on high-res MS/MS data.

max_fragment_charge, by default, will search each fragment several times against the fragment index with different charge states (up to precursor_charge - 1) to try and find candidate peptides - at the cost of increased run time. If deisotope is turned off, it is recommended to set max_fragment_charge = 1.

min_matched_peaks should be tuned per-dataset, and should be increased if chimeric searching is enabled

Recommended settings for high-res MS/MS

{
    "deisotope": true,
    "min_peaks": 15,
    "max_peaks": 150,
    "min_matched_peaks": 4,
    "max_fragment_charge": 1,
}

Recommended settings for low-res MS/MS

{
    "deisotope": false,
    "min_peaks": 15,
    "max_peaks": 150,
    "min_matched_peaks": 4,
    "max_fragment_charge": 2,
}