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Title: An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies

Abstract

The mass accuracy and peak intensity of ions detected by mass spectrometry (MS) measurements are essential to facilitate compound identification and quantitation. However, high concentration species can easily cause problems if their ion intensities reach beyond the limits of the detection system, leading to distorted and non-ideal detector response (e.g. saturation), and largely precluding the calculation of accurate m/z and intensity values. Here we present an open source computational method to correct peaks above a defined intensity (saturated) threshold determined by the MS instrumentation such as the analog-to-digital converters or time-to-digital converters used in conjunction with time-of-flight MS. In this method, the isotopic envelope for each observed ion above the saturation threshold is compared to its expected theoretical isotopic distribution. The most intense isotopic peak for which saturation does not occur is then utilized to re-calculate the precursor m/z and correct the intensity, resulting in both higher mass accuracy and greater dynamic range. The benefits of this approach were evaluated with proteomic and lipidomic datasets of varying complexities. After correcting the high concentration species, reduced mass errors and enhanced dynamic range were observed for both simple and complex omic samples. Specifically, the mass error dropped by more than 50% inmore » most cases with highly saturated species and dynamic range increased by 1-2 orders of magnitude for peptides in a blood serum sample.« less

Authors:
; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1430410
Report Number(s):
PNNL-SA-126312
Journal ID: ISSN 1387-3806; 48680; 400412000
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
International Journal of Mass Spectrometry
Additional Journal Information:
Journal Volume: 427; Journal Issue: C; Journal ID: ISSN 1387-3806
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
Environmental Molecular Sciences Laboratory

Citation Formats

Bilbao, Aivett, Gibbons, Bryson C., Slysz, Gordon W., Crowell, Kevin L., Monroe, Matthew E., Ibrahim, Yehia M., Smith, Richard D., Payne, Samuel H., and Baker, Erin S. An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies. United States: N. p., 2018. Web. doi:10.1016/j.ijms.2017.11.003.
Bilbao, Aivett, Gibbons, Bryson C., Slysz, Gordon W., Crowell, Kevin L., Monroe, Matthew E., Ibrahim, Yehia M., Smith, Richard D., Payne, Samuel H., & Baker, Erin S. An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies. United States. doi:10.1016/j.ijms.2017.11.003.
Bilbao, Aivett, Gibbons, Bryson C., Slysz, Gordon W., Crowell, Kevin L., Monroe, Matthew E., Ibrahim, Yehia M., Smith, Richard D., Payne, Samuel H., and Baker, Erin S. Sun . "An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies". United States. doi:10.1016/j.ijms.2017.11.003.
@article{osti_1430410,
title = {An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies},
author = {Bilbao, Aivett and Gibbons, Bryson C. and Slysz, Gordon W. and Crowell, Kevin L. and Monroe, Matthew E. and Ibrahim, Yehia M. and Smith, Richard D. and Payne, Samuel H. and Baker, Erin S.},
abstractNote = {The mass accuracy and peak intensity of ions detected by mass spectrometry (MS) measurements are essential to facilitate compound identification and quantitation. However, high concentration species can easily cause problems if their ion intensities reach beyond the limits of the detection system, leading to distorted and non-ideal detector response (e.g. saturation), and largely precluding the calculation of accurate m/z and intensity values. Here we present an open source computational method to correct peaks above a defined intensity (saturated) threshold determined by the MS instrumentation such as the analog-to-digital converters or time-to-digital converters used in conjunction with time-of-flight MS. In this method, the isotopic envelope for each observed ion above the saturation threshold is compared to its expected theoretical isotopic distribution. The most intense isotopic peak for which saturation does not occur is then utilized to re-calculate the precursor m/z and correct the intensity, resulting in both higher mass accuracy and greater dynamic range. The benefits of this approach were evaluated with proteomic and lipidomic datasets of varying complexities. After correcting the high concentration species, reduced mass errors and enhanced dynamic range were observed for both simple and complex omic samples. Specifically, the mass error dropped by more than 50% in most cases with highly saturated species and dynamic range increased by 1-2 orders of magnitude for peptides in a blood serum sample.},
doi = {10.1016/j.ijms.2017.11.003},
journal = {International Journal of Mass Spectrometry},
issn = {1387-3806},
number = C,
volume = 427,
place = {United States},
year = {2018},
month = {4}
}