Parameter List - michaelmarty/UniDec GitHub Wiki

This is a table of parameter names in Python and C with their corresponding GUI label and a brief description. I used AI to help with generating the shell but then went through it and did manual annotation. There may be parameters missing here. I did my best to check everything, but I may have made mistakes. In particular, I know there are some parameters that get reused by the various modes (IM, CD, IsoDec), and I'm sorry about that. I'll try at some point to go through and catch those. Please reach out if you find issues. Thanks!

Python Name	C Name	GUI Label	Description
version	version	N/A	UniDec version number
imflag	imflag	Ion Mobility	Flag for whether data is ion mobility data
cdmsflag	cdmsflag	CD-MS	Flag for if data is CD-MS data
infname	input	Input File	Input file name
outfname	output	Output File	Output file name
numit	numit	Maximum # of iterations	Number of iterations
numz	numz	# Charge States	Number of charge states
endz	endz	Charge Range	Ending charge state
startz	startz	Charge Range	Starting charge state
zzsig	zzsig	Charge Smooth Width	Charge state peak width
psig	psig	Point Smooth Width	Parameter for width used in point smoothing (not main FWHM)
beta	beta	Beta	Beta parameter for softmax artifact reduction
mzsig	mzsig	Peak FWHM (Th)	m/z peak width (FWHM)
psfun	psfun	Peak Shape Function	(0=Gaussian, 1=Lorentzian, 2=Split G/L)
psfunz	zpsfn	Charge Peak Shape Function	Same as above but for CD-MS data.
discreteplot	discreteplot	Discrete Plot	Flag creates faster but blocky looking plots (GUI only)
smashflag	smashflag	Remove Noise Peaks	Flag for whether to smash certain range of the data out (see smashlist)
massub	massub	Mass Range	Upper bound for mass
masslb	masslb	Mass Range	Lower bound for mass
msig	msig	Mass Smooth Width	Mass smooth width used when oligomer mass is set.
molig	molig	Mass Differences (Da)	Oligomer mass used in mass smoothing
massbins	massbins	Sample Mass Every (Da)	Mass bin size. Each mass point will be sampled at this spacing.
mtabsig	mtabsig	Mass List Window (Da)	When using a defined list of allowed masses, this sets the window around each that are allowed. 0, will force only exactly those masses. See masslist.
minmz	minmz	m/z	Minimum m/z
maxmz	maxmz	m/z	Maximum m/z
subbuff	subbuff	After Subtract {type} choice box	Background subtraction parameter. See next parameter for explanation.
subtype	subtype	Subtract {type} choice box	Type of background subtraction, 0=global minimum subtracted (buff turns off or on), 1=linear fit (buff sets number of starting and ending points to average) 2=curved (buff sets width of curve. Lower is more extreme buffer subtraction) 3=constant (buff is fraction of peak intensity to set threshold at)
smooth	smooth	Gaussian Smoothing	Width of Gaussian smoothing function applied to data pre-deconvolution.
mzbins	mzbins	Bin Every	Size of m/z bins for resampling. 0 will use native data sampling.
peakwindow	peakwindow	Peak Detection Range (Da)	Peak detection window
peakthresh	peakthresh	Peak Detection Threshold	Peak detection threshold
normthresh	normthresh	Normalize Peak Threshold	Flag for if the peak detection threshold should be normalized or absolute. 0 means that peakthresh is considered absolute. 1 means that peakthresh is considered normalized.
peakplotthresh	peakplotthresh	Marker Threshold	Threshold to for plotting peak markers at the edges of charge state distributions.
separation	plotsep	Species Separation	Vertical separation between plots. Set to 0 to have plots overlap perfectly.
intthresh	intthresh	Intensity Threshold	Removes noise pre-deconvolution
reductionpercent	reductionpercent	Data Reduction (%)	Removes the lowest x percent of data pre-deconvolution. Similar to intensity threshold but sets the threshold to remove a specific percent.
aggressiveflag	aggressive	Advanced Menu Best Mode vs others	Experimental parameter used for different things at different times. Repurposed for IsoDec bin size (4 vs 8). Leave at 0 for regular UniDec unless you are feeling brave.
rawflag	rawflag	Bullet for Reconvolved/Profile or Raw/Centroid	0=Reconvolved/Profile data 1=Raw/Centroid data. Not exactly a real centroiding but it allows the full peak width narrowing of the deconvolution to take over. Use higher mzsig values to drive this.
adductmass	adductmass	Adduct Mass	ESI adduct mass. Default is proton mass or minus proton mass in negative mode.
nativezub	nativezub	Native Charge Offset Range	Native charge upper bound. Uses an experimental fit of native charge vs. mass to predict the charge state for each mass species. Doesn't let the charge for a given mass to stray above the native charge + this upper bound. Used to slice an allowed swoop in the mass vs charge space.
nativezlb	nativezlb	Native Charge Offset Range	Native charge lower bound. See above except it's the native charge + this lower bound. Should be negative if you want to allow species below the native charge.
poolflag	poolflag	m/z to Mass Transformation	Parameter to control m/z to mass transformation. 0=Integrate, 1=Interpolate, 2=Smart. Integrate is best if mass is undersampled relative to m/z. Interpolate if mass is oversampled. Smart will automatically pick the right one based on the data sampling for each and is strongly encouraged.
detectoreffva	accvol	Acceleration Voltage (kV)	Detector voltage used to model and correct for lower ToF detector efficiency at higher mass values. Not sure if it really works. See refs in code and papers.
inflate	peakshapeinflate	Experimental > Experimental Parameters > Peak Shape Inflate	Peak shape inflation factor. Uses a larger peak shape for deconvolution than for peak shape reconstruction.
noiseflag	noiseflag	Report Multiple Monoisos	Actually not sure what this does... It got repurposed in IsoDec for Report Multiple Monoisotopic peaks.
linflag	linflag	Choice box below Bin Every	Defines linearization process. 0=constant m/z (integration, mzbins sets spacing between points), 1=constant resolution (integration, mzbins sets spacing for first two points, but other points are spaced to keep resolution constant with that), 2=nonlinear (mzbins sets number of points to average together), 3=Linear Interpolated (similar to 0 but interpolated), 4=Linear Resolution Interpolated (similar to 1 but interpolated)
cmap	cmap	2D Color Map	Colormap for 2D plots
peakcmap	peakcmap	Peak Color Map	Colormap for peaks as they are chosen.
spectracmap	spectracmap	Spectrum Colormap	Colormap for spectra in UniChrom and MetaUniDec.
publicationmode	publicationmode	Publication Mode	Publication mode flag to clean up plots.
isotopemode	isotopemode	Isotopes: choice box	Isotope mode. 0=Off, 1=Monoisotopic masses, 2=Average masses. Do not recommend with IsoDec now out. Will be removed soon. A better solution has always been to set molig and msig to 1, which does better anyway.
peaknorm	peaknorm	Peak Normalization	Peak normalization flag. 0=None, 1=Max, 2=Total
datanorm	datanorm	Normalize Data	Data normalization flag, 1=Normalize to 1.
baselineflag	baselineflag	N/A	Baseline subtraction flag? Not sure this is actually used...
orbimode	orbimode	Charge Scaling	For Orbitrap and FTICR detectors, the intensity is actually proportional to number of charges and not number of ions. When set to 1, this divides each intensity by the charge state to get data in number of ions.
avgpeakmasses	Avg Peak Masses	Average Mass	IsoDec flag to use average mass (1) vs. monoisotopic (0).
selection_type	Selection type	IsoDec Deconvolution Type Choice Box	Type of IsoDec data used. Peptide vs Rna vs None
filterwidth	filterwidth	IsoDec Match Tolerance (ppm)	IsoDec PPM match tolerance
zerolog	zerolog	Experimental Parameters	For smoothing in log space, you need to define a value for 0, which is normally undefined. Default is -12. Not sure there is any benefit in changing this.
doubledec	doubledec	Double Deconvolution	Double deconvolution flag to turn on DoubleDec
kernel	kernel	Open Kernel File	Text file of DoubleDec kernel template. See more about DoubleDec in Rhodopsin paper.
CDslope	CDslope	CDMS Slope	CDMS slope to intensity calibration
CDzbins	CDzbins	CDMS Charge Bin Size	CDMS bin size for charge histograms.
CDres	CDres	CDMS Charge Filtering Width	CDMS Setting for whether to use filtering of nearby m/z values in the same scan. This is the m/z distance restraint used.
CDScanStart	CDScanStart	CDMS Scan Start	CDMS first scan to use
CDScanEnd	CDScanEnd	CDMS Scan End	CDMS last scan to use
CDprethresh	CDprethresh	CDMS Import Threshold	CDMS Threshold used to remove low-intensity ions before importing them. Helps avoid memory crashes with large CD-MS data sets.
HTksmooth	HTksmooth	HT Smoothing	Hadamard transform smoothing of the EIC/TICs
CDScanCompress	CDScanCompress	CDMS Scan Compression	UniChromCD scan compression. Averages N Scans together.
HTmaxscans	HTmaxscans	HT Max Scans	Hadamard transform max scans
HToutputlb	HToutlb	HT DM Time Range	Hadamard transform time lower bound
HToutputub	HToutub	HT DM Time Range	Hadamard transform time upper bound
HTtimepad	HTtimepad	HT Time Padding	Hadamard transform time padding
HTanalysistime	HTanalysistime	HT Analysis Time	Hadamard transform total analysis time
HTxaxis	HTxaxis	N/A	Hadamard transform x-axis label (s vs. min)
HTcycleindex	HTcycleindex	N/A	Hadamard transform cycle index
HTcycletime	HTcylctime	HT Cycle Length	Hadamard transform cycle time
HTtimeshift	HTtimeshift	HT Time Shift	Hadamard transform time shift
htbit	htbit	HT Sequence Bit	Hadamard transform bit. Negative means reversed and S means shifted.
FTstart	FTstart	FT Start (Hz)	FT sweep start frequency
FTend	FTend	FT End (Hz)	FT sweep end requency
FTflatten	FTflatten	FT Flatten	FT flatten flag
FTapodize	FTapodize	FT Apodize	FT apodize flag
demultiplexmode	demultiplexmode	Demultiplex Mode	Demultiplexing mode, HT, mHT (masked), FT, aFT (absorption mode)
FTsmooth	FTsmooth	FT Post Smoothing	FT smoothing parameter applied after FT
HTmaskn	HTmaskn	HT mHT Iterations	Number of iterations of masking performed
HTwin	HTwin	HT mHT Masks/Iter	Number of masks used per iteration on mHT
csig	csig	CCS Smooth Width/Cosine Score Threshold/Charge Spread (FWHM)	CCS smooth width in Ion Mobility mode. Reused by IsoDec for Cosine Score Threshold. Reused for charge FWHM in CD-MS mode.
smoothdt	smoothdt	CD or IM: Gaussian Smoothing	Gaussian Smoothing for second dimension (either charge or drift time)
subbufdt	subbufdt	CD or IM: Baseline Subtraction	Subtraction buffer for drift time or charge dimension in CD-MS
centroided	centroided	Data is Centroided	Flag in IsoDec indicating data is centroided