Optimizing Spectroscopic Signal-to-Noise Ratio in Analysis of Data Collected by a Chromatographic/Spectroscopic System

Abstract

To get an accurate spectrum across a chromatographic peak when analyzing data collected from a chromatography/spectroscopy experiment such as liquid chromatography/mass spectrometry, it is often necessary to sum or average the spectra collected across the chromatographic peak. A common practice is to sum the spectra collected across the entire duration of the chromatographic peak. However, this practice is not ideal in terms of optimizing the signal-to-noise ratio (S/N) of the sum spectrum. In most instances, the spectral signals may be so weak at the earlier and later ends of the chromatographic peak that summing these spectra into the sum spectrum may decrease its overall S/N. This report describes some simple guidelines and methods to analyze data collected by a chromatography/spectroscopy system to achieve the maximum S/N from the available data. More specifically, to achieve a better S/N when summing spectra within one chromatographic peak, only the spectra whose relative abundance is above 38% should be included. To achieve the maximum possible S/N, a matched filter should be applied to the data before the spectra are summed.

Screening and Identification of Glyceollins and Their Metabolites by Electrospray Ionization Tandem Mass Spectrometry with Precursor Ion Scanning

“…Moreover, in LC-MS/MS experiments, the (S/N) ratios may not be maximized if spectra are averaged across the entire width of the chromatographic peak (due to weaker signals away from the center of the peak). 43 A literature example reports a 20-fold gain in sensitivity observed with direct infusion of LC fractions using multichannel acquisition, as compared to LC/MS. 44 Therefore, we suspect that the conditions employed for LC-ESI-MS/MS resulted in a detection limit just above the threshold for observation of these m/z 353, 355, and 469 signals.…”

Triple quadrupole linear ion trap mass spectrometer for the analysis of small molecules and macromolecules

“…A volume 10 µl of this fraction was infused into the mass spectrometer using a NanoMate, a silicon chip‐based device (Advion BioSciences). With infusion and multi‐channel acquisition the quality of the tandem mass spectra (signal‐to‐noise ratio) improves with the number of scans which are summed 42. The NanoMate typically operates at flow‐rates of ∼100–250 nl min −1 , allowing plenty of time to perform MS/MS optimization and acquisition.…”

Discussion on common data analysis strategies used in MS‐based proteomics

“…Kast et al have used FFT in window sizes of 10 Da combined with a correlation function that enhances the signal if intensity on other isotope peaks exists 14. It is possible to enhance signals that are hidden in the noise by using the knowledge of the periodicity of the isotope peaks 14 and by integration of the retention time in the LC‐MS profile 21. McElvain and co‐worker provide a theoretical argument stating that the optimal S / N is maximized when the selection threshold for spectral summation is 38% of the maximum signal magnitude 21.…”