Main container for the Skyline document Container for all Skyline document settings information Container for peptide settings information If true, previously measured retention times will be used to predict retention times for scheduling of future peptide measurements. Time window in minutes around a measured peak center (i.e. (start + end)/e) used in scheduling future peptide measurements. If true, ion mobility (drift time, inverse reduced ion mobility, etc.) values found in spectral libraries will be used in chromatogram extraction. Defaults to false. N.B. The use of the term drift time in the spectral library context is historical - other ion mobility types are supported so this should be understood as ion mobility in the general sense. When spectral_library_drift_times_peak_width_calc_type is set to resolving_power, ion mobility (drift time, inverse reduced ion mobility, etc.) matching tolerance for spectral library ion mobility is calculated as: For resolving power "R" at drift time "T", the width "W" of the drift time matching window centered at T is W = 2T/R When spectral_library_drift_times_peak_width_calc_type is set to linear_range, ion mobility matching tolerance is calculated as: For peak width at drift time zero "Wdt0" and peak width at drift time max "WdtMax" and max drift time "dtMax" at drift time "T", the width "W" of the drift time matching window centered at T is W = Wdt0 + (WdtMax-Wdt0)*T/dtMax Upper limit of top ranking peptided to pick per protein. Used only if peptides are ranked. This attribute is used only when there is a single internal standard and it is not "heavy". If there are multiple internal standards each is written in a <internal_standard> element. Container for transition settings information Peptide rank either by spectrum count or by the total intensity of the picked transition peaks. If there are multiple precursors, the rank of the best precursor is used. This can be an explicit value, or the best value based on measured results, or the value calculated from a linear regression. This can be the best value based on measured results, or the value calculated from a linear regression. One of "custom", "precursor", "a", "b", "c", "x", "y", "z" Peak index in the isotopic distribution of the precursor. Has a value only when fragment_type is "precursor". Value is NULL if fragment_type is "precursor" or "custom_precursor". Peak rank (by intensity) in the isotopic distribution of the precursor. Has a value only when fragment_type is "precursor". Intensity of the peak in the isotopic distribution of the precursor. Has a value only when fragment_type is "precursor". e.g. Value is 9 for y9 fragment. Has a value only when fragment_type is "precursor". Value is NULL if fragment_type is "precursor". Value is NULL if fragment_type is "precursor". Value is NULL if fragment_type is "precursor". The name of the measured ion that this transition uses (Only for reporter ions and other non proteomic transitions) Specifies the peptide picking strategy. Picks only peptides that match a library spectrum. Uses peptide filter settings instead of library spectra for picking peptides. Pick peptides that match both a library spectrum and the filters. Pick peptides that match either a library spectrum and the filters. Specifies a value associated with each library spectrum that may be used to rank matching peptides. This attribute is used only for isotope modifications. This attribute is used only for isotope modifications. This attribute is used only for isotope modifications. This attribute is used only for isotope modifications. This attribute is used only for isotope modifications. This attribute is used only for isotope modifications. This attribute is used only for isotope modifications. If "true" both modified and unmodified forms may be present in a peptide. Value of this attribute is a reference to the "name" attribute of one of the <replicate> child elements of <measured_results>. This attribute is present only if the replicate has multiple files. Average peak count ratio (proportion of transition peaks) of all the precursors of a peptide in a single sample file. Average retention time of all the precursors of a peptide in a single sample file. When true, the sample file is not to be used in calibration calculations.