Search window settings
An experimental spectrum is scanned for matches by shifting the theoretical spectrum along m/z by increments of ‘tolerance’. The start and end points of the search grid are determined by search window settings. There are two search modes: ‘absolute bounds’ and ‘fixed width’. A search mode can selected by opening a respective tab in IsoGlyph settings.
Absolute bounds
Section titled “Absolute bounds”A search window with absolute bounds starts and ends at points specified by the user. Theoretical mass of the target fragment does not matter in this case, matching is only performed based on shape. This mode is useful to identify products with unknown groups, which add an unknown offset to the spectrum. This type of search window has two parameters:
Minimum
Section titled “Minimum”Minimum needs to contain the lowest mass considered by the search algorithm. It is in atomic mass units (amu) and must be a floating point number greater than zero.
Maximum
Section titled “Maximum”Maximum needs to contain the highest mass considered by the search algorithm. It is in atomic mass units (amu) and must be a floating point number greater than zero.
Fixed width
Section titled “Fixed width”A search window with a fixed with is centered at the average theoretical mass of the target fragment and has a width specified by the used. This mode is useful to confirm the presence of known compounds. Allowing for a sufficiently wide search window is still important even when matching known compounds because a systematic mass measurement error may apply. This type of search window has only one paremeter:
Width needs to contain the width of the search window. It is in atomic mass units (amu) and must be a floating point number greater than zero.