This project is archived and no longer maintained.
|Description||Graphical tools to aid users in choosing critical parameters for Cromwell spectra denoising|
|Platforms||Platforms supporting Matlab|
|Last updated||12th March 2004|
|Citation||Coombes KR, Tsavachidis S, Morris JS, Baggerly KA, Hung MC, Kuerer HM. (2005). Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform. Proteomics, 5(16), 4107-4117. https://doi.org/10.1002/pmic.200401261|
|Help and Support|
|Contact||Kevin R. Coombs|
Cromwell is an implementation of our algorithms for low-level processing of mass spectrometry proteomics data. Cromwell uses the undecimated discrete wavelet transform to denoise spectra; a critical parameter is the threshold to use for denoising. We have developed graphical tools to aid users in making this decision.
The following Matlab .m function files are in the download package:
Please set the Matlab path to include the directory containing the scripts. You can find instructions on how to do so here.
This documentation is included in the readme file of the download package.
This package consists of two MATLAB functions to assist users with choosing the thresholds for wavelet denoising using the Cromwell package.
 function [smoothed, thresholds] = sizerPrep(inten, thresholds, infinity) This function takes three inputs inten = the raw spectrum intensities thresholds = a vector of threshold settings to apply (default = 4:100) infinity = a really large threshold setting (default = 1000) The output consists of two objects smoothed is a matrix containing the smooth spectra for all thresholds thresholds is the vector of thresholds The outputs can be used as inputs to the corresponding plotting routine, sizerPlot.  function sizerPlot(spec, smoothed, thresholds, sml, range) The inputs of this function are spec = the raw intensity spectrum smoothed = a matrix of smoothed spectra from sizerPrep thresholds = a vector of thresholds from sizerPrep sml = a vector of thresholds that should be displayed range = a vector of spectrum time points to display The function returns no outputs. Instead, it produces a graph containing a heatmap of the deviations of the smooth spectra from the "infinitely smoothed" spectrum, along with overlays of the raw spectrum and the smooths corresponding to the minimal and maximal displayed thresholds.
The output of the first script is passed as input to the second, along with display ranges. Atypical output is displayed below. The horizontal axis is the time index in the spectrum; the vertical axis for the heatmap is te threshold. Colors indicate the deviation of the spectrum (at that threshold level) from an “infinitely” smoothed spectrum, represented by the overlaid white curve. The raw spectrum is overlaid in black, along with the smooth curves corresponding to the minimum (in red) and maximum (in green) displayed thresholds
Cromwell is copyrighted by the MD Anderson Cancer Center; the licensing details are straightforward, considering that Cromwell is free software from an academic institution.
This is the "cromwell" mass spec analysis package. Released - <1 March 2004> CONDITIONS FOR USE: Copyright (c) 2003, 2004 UT MD Anderson Cancer Center. All rights reserved. This software is distributed and licensed to you on a non-exclusive basis, free-of-charge. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistribution of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistribution in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. All advertising materials mentioning features or use of this software must display the following acknowledgment: This product includes software developed by the University of Texas MD Anderson Cancer Center, Houston, Texas and its contributors. 4. Neither the name of the University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER, HOUSTON, TEXAS, AND CONTRIBUTORS AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL MD ANDERSON OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTIONS) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE), PRODUCT LIABILITY, OR OTHERWISE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.