Suppression correction and characteristic study in liquid chromatography/Fourier transform mass spectrometry measurements

Abstract

Analysis of peptide profiles from liquid chromatography/Fourier transform mass spectrometry (LC/FTMS) reveals a nonlinear distortion in intensity. Investigation of the measured C13/C12 ratios comparing with theoretical ones shows that the nonlinearity can be attributed to signal suppression of low abundance peptide peaks. We find that the suppression is homogenous for different isotopes of identical peptides but non-homogenous for different peptides. We develop an iterative correction algorithm that corrects the intensity distortions for peptides with relatively high abundance. This algorithm can be applied in a wide range of applications using LC/FTMS. We also analyze the distortion characteristics of the instrument for lower abundance peptides, which should be considered when interpreting quantification results of LC/FTMS.

An SILAC quantification algorithm for LC-FTMS

“…We can see that including more isotopes introduces larger bias in measured H/L ratios. This agrees very well with our previous research on instrument suppression [5]. On the other hand, using two or three isotopes provides the least variance, which agrees with our analysis on variance reduction.…”

“…In this sense, the more isotopes we consider, the lower the variance on abundance estimation. However, in [5], it is revealed that most peptide intensities are suppressed to a degree. Thus, to reduce the distortion on ratio measurement, it is better to use fewer isotopes.…”

“…[4]. In addition, we considered the problem of instrument suppression present in Fourier-Transform-Mass-Spectrometry (FTMS) [5], which reveals that intensity measurements in FTMS are generally suppressed randomly. Lastly, we consider an accurate noise model which has been largely ignored in the past [6], [7].…”

Improved Quantification of Labeled LC-MS

“…For example, as illustrated in Figure 3, our past research shows severe distortion of normalized 12 C/ 13 C ratios in a LC-MS measurement [1]. Without distortion, the normalized ratios as listed in (1) should be centered at one, but in Figure 3 the ratios are mostly under one.…”

“…Without distortion, the normalized ratios as listed in (1) should be centered at one, but in Figure 3 the ratios are mostly under one. 12 13 .…”