Analysis of Overlapped and Noisy Hydrogen/Deuterium Exchange Mass Spectra

This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of the American Chemical Society, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1007/s13361-013-0727-5.Noisy and overlapped mass spectrometry data hinders the sequence coverage that can be obtained from Hydrogen Deuterium exchange analysis, and places a limit on the complexity of the samples that can be studied by this technique. Advances in instrumentation have addressed these limits, but as the complexity of the biological samples under investigation increases, these problems are reencountered. Here we describe the use of binomial distribution fitting with asymmetric linear squares regression for calculating the accurate deuterium content for mass envelopes of low signal or that contain significant overlap. The approach is demonstrated with a test data set of HIV Env gp140 wherein inclusion of the new analysis regime resulted in obtaining exchange data for 42 additional peptides, improving the sequence coverage by 11%. At the same time, the precision of deuterium uptake measurements was improved for nearly every peptide examined. The improved processing algorithms also provide an efficient method for deconvolution of bimodal mass envelopes and EX1 kinetic signatures. All these functions and visualization tools have been implemented in the new version of the freely available software, HX-Express v2

Alterations in the blood velocity profile influence the blood flow response during muscle contractions and relaxations

The present study examined the influences of the muscle contraction (MCP) and relaxation (MRP) phases, as well as systole and diastole, on the blood velocity profile and flow in the conduit artery at different dynamic muscle contraction forces. Eight healthy volunteers performed one-legged dynamic knee-extensor exercise at work rates of 5, 10, 20, 30, and 40 W at 60 contractions per minute. The time- and space-averaged, amplitude-weighted, mean (V-mean) and maximum (V-max) blood flow velocities were continuously measured in the common femoral artery during the cardiosystolic (CSP) and cardiodiastolic (CDP) phases during MCP and MRP, respectively. The V-max/V-mean ratio was used as a flow profile index where a ratio of approximately (similar to) 1 indicates a "flat" velocity profile, and a ratio significantly greater than (>>) 1 indicates a "parabolic" velocity profile. At rest, a "steeper' parabolic velocity profile was found during the CDP (ratio: 1.75 +/- 0.06) than during the CSP (ratio: 1.31 +/- 0.02). During the MRP of exercise, the V-max/V-mean ratio shifted to be less steep (p = 20W during the CDP (ratio: 2.15-2.52) and >= 30W during the CSP (ratio: 1.49-1.77), potentially because of a greater retrograde flow component. A higher blood flow furthermore appeared during the MRP compared to during the MCP, coinciding with a greater uniformity of the red blood cells moving at higher blood velocities during the MRP. Thus part of the difference in the magnitude of blood flow during the MRP vs. MCP may be due to the alterations of the blood velocity flow profile