How do I let the search engine know my mass accuracy window and my elemental formula constraints?
There are no parameters that need to be set. The mass accuracy window of IndexSearch varies with molecular weight. If the experimental mass of your protonated or deprotonated molecule is off by more than this value, then the search engine will not find the correct compound. Over these mass ranges the following mass windows (in milliDaltons) are used: 86 to 99: 1.0 100 to 199: 1.9 200 to 299: 2.8 300 to 399: 3.6 400 to 499: 4.0 500 to 599: 4.2 600 to 699: 4.0 700 to 799: 3.4 800 to 899: 2.2 900 to 990: 1.0 More accuracy is required to search at higher masses, but fortunately less than 2% of the compounds indexed are between masses 601 and 990. Within the mass window, the scoring system takes into account the mass error of the fragment ions and having more accurate data will therefore help to pinpoint the correct matching compound in the index. The window actually used (in ppm) will print out on your report. No elemental formula constraints are needed other those imposed by the mass spec
