Correcting for Naturally Occurring Mass Isotopologue Abundances in Stable-Isotope Tracing Experiments with PolyMID

Stable-isotope tracing is a method to measure intracellular metabolic pathway utilization by feeding a cellular system a stable-isotope-labeled tracer nutrient. The power of the method to resolve differential pathway utilization is derived from the enrichment of metabolites in heavy isotopes that are synthesized from the tracer nutrient. However, the readout is complicated by the presence of naturally occurring heavy isotopes that are not derived from the tracer nutrient. Herein we present an algorithm, and a tool that applies it (PolyMID-Correct, part of the PolyMID software package), to computationally remove the influence of naturally occurring heavy isotopes. The algorithm is applicable to stable-isotope tracing data collected on low- and high- mass resolution mass spectrometers. PolyMID-Correct is open source and available under an MIT license.

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Rapid high mass resolution mass spectrometry using matrix-assisted ionization

Methods ◽

10.1016/j.ymeth.2016.01.019 ◽

2016 ◽

Vol 104 ◽

pp. 63-68 ◽

Cited By ~ 16

Author(s):

Sarah Trimpin ◽

Shameemah Thawoos ◽

Casey D. Foley ◽

Daniel W. Woodall ◽

Jing Li ◽

...

Keyword(s):

Mass Spectrometry ◽

Mass Resolution ◽

High Mass ◽

High Mass Resolution ◽

Resolution Mass

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Protein turnover measurement using selected reaction monitoring-mass spectrometry (SRM-MS)

Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences ◽

10.1098/rsta.2015.0362 ◽

2016 ◽

Vol 374 (2079) ◽

pp. 20150362 ◽

Cited By ~ 1

Author(s):

Stephen W. Holman ◽

Dean E. Hammond ◽

Deborah M. Simpson ◽

John Waters ◽

Jane L. Hurst ◽

...

Keyword(s):

Mass Spectrometry ◽

Protein Turnover ◽

Tricarboxylic Acid Cycle ◽

High Mass ◽

Selected Reaction Monitoring ◽

Reaction Monitoring ◽

Turnover Rates ◽

Mass Spectrometers ◽

High Mass Resolution ◽

Sensitivity And Selectivity

Protein turnover represents an important mechanism in the functioning of cells, with deregulated synthesis and degradation of proteins implicated in many diseased states. Therefore, proteomics strategies to measure turnover rates with high confidence are of vital importance to understanding many biological processes. In this study, the more widely used approach of non-targeted precursor ion signal intensity (MS1) quantification is compared with selected reaction monitoring (SRM), a data acquisition strategy that records data for specific peptides, to determine if improved quantitative data would be obtained using a targeted quantification approach. Using mouse liver as a model system, turnover measurement of four tricarboxylic acid cycle proteins was performed using both MS1 and SRM quantification strategies. SRM outperformed MS1 in terms of sensitivity and selectivity of measurement, allowing more confident determination of protein turnover rates. SRM data are acquired using cheaper and more widely available tandem quadrupole mass spectrometers, making the approach accessible to a larger number of researchers than MS1 quantification, which is best performed on high mass resolution instruments. SRM acquisition is ideally suited to focused studies where the turnover of tens of proteins is measured, making it applicable in determining the dynamics of proteins complexes and complete metabolic pathways. This article is part of the themed issue ‘Quantitative mass spectrometry’.

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Development of high-spatial and high-mass resolution mass spectrometric imaging (MSI) and its application to the study of small metabolites and endogenous molecules of plants

10.2172/1048509 ◽

2012 ◽

Author(s):

Ji Hyun Jun

Keyword(s):

Mass Spectrometric ◽

Mass Resolution ◽

High Mass ◽

Mass Spectrometric Imaging ◽

High Mass Resolution ◽

Resolution Mass

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Direct human breath analysis by secondary nano-electrospray ionization ultrahigh-resolution mass spectrometry: Importance of high mass resolution and mass accuracy

Rapid Communications in Mass Spectrometry ◽

10.1002/rcm.7794 ◽

2017 ◽

Vol 31 (3) ◽

pp. 301-308 ◽

Cited By ~ 15

Author(s):

Xue Li ◽

Lei Huang ◽

Hui Zhu ◽

Zhen Zhou

Keyword(s):

Mass Spectrometry ◽

Electrospray Ionization ◽

Breath Analysis ◽

Mass Accuracy ◽

Mass Resolution ◽

High Mass ◽

Human Breath ◽

Ultrahigh Resolution ◽

High Mass Resolution ◽

Resolution Mass

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THEORETICAL AND EXPERIMENTAL STUDY OF HIGH-MASS HIGH-RESOLUTION MASS SPECTROMETERS

Advances in Mass Spectrometry ◽

10.1016/b978-0-08-009210-2.50010-9 ◽

1959 ◽

pp. 44-65 ◽

Cited By ~ 6

Author(s):

H.G. VOORHIES ◽

C.F. ROBINSON ◽

L.G. HALL ◽

W.M. BRUBAKER ◽

C.E. BERRY

Keyword(s):

Experimental Study ◽

High Resolution ◽

High Mass ◽

Mass Spectrometers ◽

High Resolution Mass ◽

Resolution Mass

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Multimodal Chemical Analysis of the Brain by High Mass Resolution Mass Spectrometry and Infrared Spectroscopic Imaging

Analytical Chemistry ◽

10.1021/acs.analchem.8b02913 ◽

2018 ◽

Vol 90 (19) ◽

pp. 11572-11580 ◽

Cited By ~ 19

Author(s):

Elizabeth K. Neumann ◽

Troy J. Comi ◽

Nicolas Spegazzini ◽

Jennifer W. Mitchell ◽

Stanislav S. Rubakhin ◽

...

Keyword(s):

Mass Spectrometry ◽

Chemical Analysis ◽

Spectroscopic Imaging ◽

Mass Resolution ◽

High Mass ◽

High Mass Resolution ◽

Infrared Spectroscopic ◽

Infrared Spectroscopic Imaging ◽

The Brain ◽

Resolution Mass

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Development of high-spatial and high-mass resolution mass spectrometric imaging (MSI) and its application to the study of small metabolites and endogenous molecules of plants

10.31274/etd-180810-1222 ◽

2012 ◽

Author(s):

Ji Hyun Jun

Keyword(s):

Mass Spectrometric ◽

Mass Resolution ◽

High Mass ◽

Mass Spectrometric Imaging ◽

High Mass Resolution ◽

Resolution Mass

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Simultaneous isotope dilution quantification and metabolic tracing of deoxyribonucleotides by liquid chromatography high resolution mass spectrometry

10.1101/454322 ◽

2018 ◽

Cited By ~ 1

Author(s):

Rostislav Kuskovsky ◽

Raquel Buj ◽

Peining Xu ◽

Samuel Hofbauer ◽

Mary T Doan ◽

...

Keyword(s):

Mass Spectrometry ◽

Stable Isotope ◽

Isotope Dilution ◽

High Resolution Mass Spectrometry ◽

Reversed Phase ◽

Pentose Phosphate ◽

High Mass ◽

Mass Analyzer ◽

Isotope Tracing ◽

Metabolic Tracing

AbstractQuantification of cellular deoxyribonucleoside mono-(dNMP), di-(dNDP), triphosphates (dNTPs) and related nucleoside metabolites are difficult due to their physiochemical properties and widely varying abundance. Involvement of dNTP metabolism in cellular processes including senescence and pathophysiological processes including cancer and viral infection make dNTP metabolism an important bioanalytical target. We modified a previously developed ion pairing reversed phase chromatography-mass spectrometry method for the simultaneous quantification and 13C isotope tracing of dNTP metabolites. dNMPs, dNDPs, and dNTPs were chromatographically resolved to avoid mis-annotation of in-source fragmentation. We used commercially available 13C15N-stable isotope labeled analogs as internal standards and show that this isotope dilution approach improves analytical figures of merit. At sufficiently high mass resolution achievable on an Orbitrap mass analyzer, stable isotope resolved metabolomics allows simultaneous isotope dilution quantification and 13C isotope tracing from major substrates including 13C-glucose. As a proof of principle, we quantified dNMP, dNDP and dNTP pools from multiple cell lines. We also identified isotopologue enrichment from glucose corresponding to ribose from the pentose-phosphate pathway in dNTP metabolites.

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