multiplierz.mztools.chargeTransform

Charge deconvolution of intact protein spectra is a difficult problem; a tricky math problem (namely, finding a analyte mass that, for some charge series, produces the correct set of charged peaks) is combined with noisy data (since the mass peaks in the spectrum can be broad, contain interference, and represent multiple distinct analytes.) Since charge deconvolution is prone to error in adverse instances, rather than return a set numbers specifying the analyte mass(es), the Multiplierz charge deconvolution tools return a plot of the deconvolution solution, so that a human researcher can immediately confirm the validity of the result.

chargeTransform(inputFile,outputFile = None, mzRangeStart = 300,mzRangeEnd = 2000, massRangeStart = 10000, 
                massRangeEnd = 100000,speciesCount = 5,removalArea = 2, minimumPeaks = 8, peakIterations = 2, zcLabelCount = 10,
                zoomLabelCount = 5, segmentMode = False, startSegment = 0, segmentSize = 5, consolidate = False, recalSlope = 0,
                recalIntercept = 0, smoothWidth = 0)

Invokes the charge deconvolution algorithm, returning either a Matplotlib plot instance or the path to an output image file (depending on the outputfile parameter.) Parameters are:

• mzRangeStart, mzRangeEnd : Beginning and ending of the m/z range that will be considered when looking for ion peaks.

• massRangeStart, massRangeEnd : Beginning and ending of the possible analyte mass range. Molecules outside of this range will not be found, or may produce spurious results.

• speciesCount : Maximum number of chemical species that will be investigated in a single run.

• removalArea : The M/Z region around each peak that is removed from consideration when the peak is accounted for.

• minimumPeaks : Minimum peaks corresponding to a given mass that must be found for that mass to be considered a valid hit.

• peakIterations : Iterations of the peak-finding algorithm performed before analysis. 2 is typically a good number.

• zcLabelCount : Maximum number of chemical species that will be labelled on the zero-charge spectrum results.

• segmentMode : If False, chargeTransform takes a spectrum averaged over the region of greatest intensity in the time dimension. If True, chargeTransform performs multiple analyses, each over a different sequential segment of scan time.

• segmentSize : Length in minutes of a analysis segment (only used if segmentMode == True.)

• startSegment : The segment at which chargeTransform will start performing analyses (only used if segmentMode == True.)

• consolidate : If True, all output files will be put in the same output (only used if output type is .ppt and segmentMode == True.)

• recalSlope : Slope of the correction line applied to scan mzs; 0 applies no mz-varying correction.

• recalIntercept : Y-intercept point of the correction line applied to the scan mzs; 0 applies no constant correction.

• smoothWidth : The width of the window used in the Savitzky-Golay smoothing process on the zero-charge spectrum. Enter 0 or None for no smoothing.