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Claesen, Jürgen; Dittwald, Piotr; Burzykowski, Tomasz; Valkenborg, Dirk

doi:10.1007/s13361-012-0405-z

Cited by 9 publications

(12 citation statements)

References 6 publications

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“…As a result, the latest version of the IUPAC standard is not always used in calculating the theoretical masses or isotope distribution of biomolecules. Additionally, several isotope distribution calculators use different definitions, as was reported by Claesen et al The effect of these deviations has been briefly illustrated by Claesen et al…”

Section: Methodology and Resultsmentioning

confidence: 94%

“…As a result, the latest version of the IUPAC standard is not always used in the theoretical masses or isotope distribution of biomolecules. Additionally, several isotope distribution calculators use different definitions, as was reported by Claesen et al 1 The effect of these deviations has been briefly illustrated by Claesen et al 2 In order to avoid future confusion, vendors, software developers and regulatory agencies could agree to use a centralized repository or a controlled vocabulary to update this definition in their software automatically. In case one or more molecules are known, one can use an in-silico recalibration method 26 to correct for the mass shifts caused by differing elemental isotope definitions.…”

Section: ■ Methodology and Resultsmentioning

confidence: 99%

“…In addition to these “natural” deviations, differences between various standards, such as IUPAC and NIST, and between the elemental isotope definitions used by instrument vendors and software developers , can be observed. These discrepancies can lead to confusion and can hamper the interoperability of MS-related software tools.…”

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confidence: 99%

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Differences in the Elemental Isotope Definition May Lead to Errors in Modern Mass-Spectrometry-Based Proteomics

Claesen

Lermyte²,

Sobott³

et al. 2015

Anal. Chem.

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The elemental isotope definition used to calculate the theoretical masses and isotope distribution of (bio)molecules is considered to be a fixed, universal standard in mass-spectrometry-based proteomics. However, this is an incorrect assumption. In view of the ongoing advances in mass spectrometry technology, and in particular the ever-increasing mass precision, the elemental isotope definition and its variations should be taken into account. We illustrate the effect of the elemental isotope uncertainty on the theoretical and experimental masses with theoretical calculations and examples.

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Section: Methodology and Resultsmentioning

confidence: 94%

Section: ■ Methodology and Resultsmentioning

confidence: 99%

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Differences in the Elemental Isotope Definition May Lead to Errors in Modern Mass-Spectrometry-Based Proteomics

Claesen

Lermyte²,

Sobott³

et al. 2015

Anal. Chem.

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“…Note that large averagine molecules can be helpful to observe the trend in performance; however, in practice, heavy molecules can be less precise due to the fluctuations of isotope abundances. 9,11 …”

Section: (3) Software Platform and Implementationmentioning

confidence: 99%

Comment on “Computation of Isotopic Peak Center-Mass Distribution by Fourier Transform”

Dittwald

Zaia

et al. 2013

Anal. Chem.

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“…The advantage of BRAIN lies in its simple implementation and has been shown to be as accurate as existing methods: Emass and SIRIUS [ 4 , 5 , 7 , 9 , 23 , 24 ]. However, it has been found by [ 6 ] that the computational complexity is asymptotically suboptimal in comparison with their fast Fourier-based algorithm.…”

Section: Introductionmentioning

confidence: 99%

BRAIN 2.0: Time and Memory Complexity Improvements in the Algorithm for Calculating the Isotope Distribution

Dittwald

Valkenborg

2014

J. Am. Soc. Mass Spectrom.

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Recently, an elegant iterative algorithm called BRAIN (Baffling Recursive Algorithm for Isotopic distributioN calculations) was presented. The algorithm is based on the classic polynomial method for calculating aggregated isotope distributions, and it introduces algebraic identities using Newton-Girard and Viète’s formulae to solve the problem of polynomial expansion. Due to the iterative nature of the BRAIN method, it is a requirement that the calculations start from the lightest isotope variant. As such, the complexity of BRAIN scales quadratically with the mass of the putative molecule, since it depends on the number of aggregated peaks that need to be calculated. In this manuscript, we suggest two improvements of the algorithm to decrease both time and memory complexity in obtaining the aggregated isotope distribution. We also illustrate a concept to represent the element isotope distribution in a generic manner. This representation allows for omitting the root calculation of the element polynomial required in the original BRAIN method. A generic formulation for the roots is of special interest for higher order element polynomials such that root finding algorithms and its inaccuracies can be avoided.Graphical abstractᅟElectronic supplementary materialThe online version of this article (doi:10.1007/s13361-013-0796-5) contains supplementary material, which is available to authorized users.

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Reply to the Comment on:

Cited by 9 publications

References 6 publications

Differences in the Elemental Isotope Definition May Lead to Errors in Modern Mass-Spectrometry-Based Proteomics

Differences in the Elemental Isotope Definition May Lead to Errors in Modern Mass-Spectrometry-Based Proteomics

Comment on “Computation of Isotopic Peak Center-Mass Distribution by Fourier Transform”

BRAIN 2.0: Time and Memory Complexity Improvements in the Algorithm for Calculating the Isotope Distribution

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