The basic steps to run iFAMS analysis through the Unidec window.  I've included a "test" file (a DMPC nanodisc spectrum), and currently have it coded to only open .txt files

1.) Under "File", if you click "load spectrum", it should prompt a file finder to load a mass spectrum. It will plot the data in figure 1.
2.) Now click "FFT".  This will Fourier transform the data, and plot it in the figure 2, along with iFAMS initial estimates for local maxima in the Fourier domain. 
3.) There should be small red dots at the tops of the peaks in the Fourier spectrum. iFAMS is set up to find peaks based on local maxima in the Fourier spectrum. The defaults for finding these peak maxima in iFAMS have been chosen such that they are a realistic distance apart for subunits weighing a few hundred Da.
4.) The peaks (representing fundamental frequencies for the charge states present in the Nanodisc mass spectrum) that we are looking for have been identified, but other peaks before and after those peaks have also been found.  We will want to correct that before calculating charge states and sub-unit mass.  The program calculates the charge states and subunit mass using the first peak it finds in the Fourier spectrum, so we want to adjust the maxima finder such that the first charge state peak you want to use is the first dot in the spectrum.
5.) In order to correct the peak maxima, we will adjust original preset values that the program uses when it finds peaks.  These values can be found at the bottom, labeled "Minimum Frequency", "Minimum Height", and "Delta".
6.) "Minimum Frequncy" is a cutoff in the xaxis, and is basically sets a starting point for where to start looking for maxima.  For example, if you type "0.01", this means that iFAMS looks for maxima at frequencies 0.01 and above, and neglects anything below 0.01. Go ahead and type that in.   
7.) "Minimum Height" is a cutoff on the y axis. It's uses largest amplitude in the Fourier domain, and the cutoff is a percentage of this largest peak.  For example, if the largest peak has an amplitude of "200", and you type 25, it will look for local maxima above 50, or 25% of 200. Anything below it neglects. Type "20" in there for now.
8.) "Delta" is the minimum spacing between local maxima, and is based on the # of Data points.  In other words, if Delta is set to "5", once iFAMS locates a local maxima, it will only look for another local maxima 5 data points before and after the original local maxima. Type "5" for now.
9.) "5" is already the default value for "Delta".  Even though this is the default value, you will still need to type a value for all three settings in order to re-find peaks.
10.) Click "Recalc. Maxima Finder". You will now see the dots turn blue, and the peaks that we are interested in are now the first peaks in the Fourier spectra. In future spectra, you may need to play with the previous three values to select the peaks you want.  
11.) Click "Cacl. Z and Subunit", and iFAMS will calculate the charge states and subunit mass.  Dots it uses for this turn from blue to green.  I only have this printing the terminal for now, mostly because I'm not where to put it in the GUI.  I figured I'd let you guys decide how to go about that.  It should find [12, 13, 14, 15], [12.056603773584914, 13.075471698113217, ...]" and a submass of 677....
12.)At this point, you can now click "run iFAMS analysis". It will resconstruct the charge state specific parts, as well as plot a zero charge spectrum. 
13.)These plots are made using the absolute value of the data.  You can plot the real data by clicking the check mark that says "plot real data".
14.) I've also included the Fourier filter.  To run this, you use "# of zero frequency data" and "# of harmonics for filter" In this case, "zero frequnecy data" corresponds to the number of 1+ frequency units to include with the zero frequency data.  To make this clear, as an example, lets say you have peaks at frequencies 0.6, 0.7,0.8 and 0.9.  This would tell you that you have 6+,7+,8+,and 9+, with a 1+ frequency at 0.1.  typing in "3" under zero frequency data means that ever data point before "0.3", or 3 times 0.1, will be used for the zero frequency calculation. # of harmonics used is just what it sounds like, it's how many harmonics to include in the filter.  I generally find the more resolved harmonics included, the better.  This is just a number, where if you type 3 for example, that iFAMS will use the 1st, 2nd, and 3rd harmonics.  Because you need the charge state/frequency information to run this, Charge states and subunit mass has to be calculated first before you can run this.  For now, type in three for both and click "Fourier Filter"
15.) "Harmonic Average" is the technique we just outlined in our most recent paper, but it's the method of averaging higher harmonics when reconstructing the charge state specific distributions.  Similar to the filter, this is a number that defines the range of harmonics to use.  For example, typing 3 uses the 1st, 2nd, and 3rd harmonics.   
 



 