Development of matrix assisted laser desorption ionization-ion mobility-orthogonal time-of-flight mass spectrometry as a tool for proteomics

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Title: Development of matrix assisted laser desorption ionization-ion mobility-orthogonal time-of-flight mass spectrometry as a tool for proteomics
Author: Ruotolo, Brandon Thomas
Abstract: Separations coupled to mass spectrometry (MS ) are widely used for large -scale protein identification in order to reduce the adverse effects of analyte ion suppression , increase the dynamic range , and as a deconvolution technique for complex datasets typical of cellular protein complements . In this work , matrix assisted laser desorption -ionization is coupled with ion mobility (IM ) separation for the analysis of biological molecules . The utility of liquid -phase separations coupled to MS lies in the orthogonality of the two separation dimensions for all analytes . The data presented in this work illustrates that IM -MS relies on the correlation between separation dimensions for different classes (either structural or chemical ) of analyte ions to obtain a useful separation . For example , for a series of peptide ions of increasing mass -to -charge (m /z ) a plot drift time in the IM drift cell vs . m /z increases in a near -linear fashion , but DNA or lipids having similar m /z values will have very different IM drift time -m /z relationships , thus drift time vs . m /z can be used as a qualitative tool for compound class identification . In addition , IM -MS is applied to the analysis of large peptide datasets in order to determine the peak capacity of the method for bottom -up experiments in proteomics , and it is found that IM separation increases the peak capacity of an MS -only experiment by a factor of 5 -10 . The population density of the appearance area for peptides is further characterized in terms of the gas -phase structural propensities for tryptic peptide ions . It is found that a small percentage ( ~3 % ) of peptide sequences form extended (i .e . , helical or & #946 ; -sheet type ) structures in the gas -phase , thus influencing the overall appearance area for peptide ions . Furthermore , the ability of IM -MS to screen for the presence of phosphopeptides is characterized , and it is found that post translationally modified peptides populate the bottom one -half to one -third of the total appearance area for peptide ions . In general , the data presented in this work indicates that IM -MS offers dynamic range and deconvolution capabilities comparable to liquid -phase separation techniques coupled to MS on a time scale (ms ) that is fully compatible to current MS , including TOF -MS , technology .
URI: http : / /hdl .handle .net /1969 .1 /2203
Date: 2005-08-29

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Development of matrix assisted laser desorption ionization-ion mobility-orthogonal time-of-flight mass spectrometry as a tool for proteomics. Available electronically from http : / /hdl .handle .net /1969 .1 /2203 .

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