A hierarchical algorithm for calculating the isotopic fine structures of molecules

Li, Long; Kresh, Joshua A.; Karabacak, Murat; Cobb, Jennifer; Agar, Jeffrey N.; Hong, Pengyu

doi:10.1016/j.jasms.2008.08.008

Cited by 27 publications

(27 citation statements)

References 28 publications

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“…IsoPro and NeutronCluster report a peak with the smallest mass, followed by Mercury, Emass, IsoDalton, and BRAIN. Depending on the shape of the true aggregated isotopic distribution, the different number and location of the reported peaks may lead to a difference between the value of the average mass computed for a particular algorithm and the theoretical value, obtained from Equation (25). For the case presented in Figure 1, the difference is small, though visible for IsoPro.…”

Section: Results Of the Comparisonmentioning

confidence: 95%

“…The average mass is computed according to the following definition: Table 4 presents the results of the comparison of the theoretical average mass, as computed in Equation (25), and the weighted average based upon the predicted masses and occurrence probabilities for all peaks returned by a particular algorithm. There is virtually no difference between the two average values for BRAIN and for Emass.…”

Section: Results Of the Comparisonmentioning

confidence: 99%

“…For large molecules, the calculation of exact center-masses of aggregated variants becomes fundamental, and the calculation is taken care of by our method. When information about the isotopic fine structure is required, other methods proposed in (e.g., [24], [25], [26], or [21]) can be used. If the molecule is not too large, the multinomial expansion [10] can be applied to infer the isotopic fine structure.…”

Section: Results Of the Comparisonmentioning

confidence: 99%

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An Efficient Method to Calculate the Aggregated Isotopic Distribution and Exact Center-Masses

Claesen

Dittwald

Burzykowski

et al. 2012

J. Am. Soc. Mass Spectrom.

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In this article, we present a computation-and memory-efficient method to calculate the probabilities of occurrence and exact center-masses of the aggregated isotopic distribution of a molecule. The method uses fundamental mathematical properties of polynomials given by the Newton-Girard theorem and Viete's formulae. The calculation is based on the atomic composition of the molecule and the natural abundances of the elemental isotopes in normal terrestrial matter. To evaluate the performance of the proposed method, which we named BRAIN, we compare it with the results obtained from five existing software packages (IsoPro, Mercury, Emass, NeutronCluster, and IsoDalton) for 10 biomolecules. Additionally, we compare the computed mass centers with the results obtained by calculating, and subsequently aggregating, the fine isotopic distribution for two of the exemplary biomolecules. The algorithm will be made available as a Bioconductor package in R, and is also available upon request.

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Section: Results Of the Comparisonmentioning

confidence: 95%

Section: Results Of the Comparisonmentioning

confidence: 99%

Section: Results Of the Comparisonmentioning

confidence: 99%

See 1 more Smart Citation

An Efficient Method to Calculate the Aggregated Isotopic Distribution and Exact Center-Masses

Claesen

Dittwald

Burzykowski

et al. 2012

J. Am. Soc. Mass Spectrom.

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“…These values do not directly reflect turnover rates because they underestimate degradation of heavy 15 N species and hence the actual synthesis/degradation rate (36). They do also not reflect the % of 15 N incorporation (57, 58), a complex calculation process that is not available in an automated manner and thus not implemented here. Nevertheless, RIA also called q-value has often been used as the basis for turnover calculations (59, 60).…”

Section: Resultsmentioning

confidence: 99%

Drought and Recovery: Independently Regulated Processes Highlighting the Importance of Protein Turnover Dynamics and Translational Regulation in Medicago truncatula

Lyon

Castillejo

Mehmeti-Tershani

et al. 2016

Molecular & Cellular Proteomics

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Climate change in conjunction with population growth necessitates a systems biology approach to characterize plant drought acclimation as well as a more thorough understanding of the molecular mechanisms of stress recovery. Plants are exposed to a continuously changing environment. Extremes such as several weeks of drought are followed by rain. This requires a molecular plasticity of the plant enabling drought acclimation and the necessity of deacclimation processes for recovery and continuous growth.During drought stress and subsequent recovery, the metabolome and proteome are regulated through a sequence of molecular processes including synthesis and degradation and molecular interaction networks are part of this regulatory process. In order to study this complex regulatory network, a comprehensive analysis is presented for the first time, investigating protein turnover and regulatory classes of proteins and metabolites during a stress recovery scenario in the model legume Medicago truncatula. The data give novel insights into the molecular capacity and differential processes required for acclimation and deacclimation of severe drought stressed plants.Functional cluster and network analyses unraveled independent regulatory mechanisms for stress and recovery with different dynamic phases that during the course of recovery define the plants deacclimation from stress. The combination of relative abundance levels and turnover analysis revealed an early transition phase that seems key for recovery initiation through water resupply and is independent from renutrition. Thus, a first indication for a metabolite and protein-based load capacity was observed necessary for the recovery from drought, an important but thus far ignored possible feature toward tolerance. The data indicate that apart from the plants molecular stress response mechanisms, plasticity may be related to the nutritional status of the plant prior to stress initiation. A new perspective and possible new targets as well as metabolic mechanisms for future plant-bioengineering toward enhanced drought stress tolerance are presented.

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“…In collaborating Dr. Agar of Chem istry at Brandeis, we have developed new tools for analyzing mass spectrometry data (Li, Kresh et al 2008) (Karabacak, Li et al 2009). …”

Section: (C) Mass Spectrometry Data Analysismentioning

confidence: 99%

Functions and Mechanisms of Sleep in Flies and Mammals

Rosbash¹

2009

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Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to Department of Defense, Washington Headquarters Services, Directorate for Information Operations and Reports (0704-0188), 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. REPORT DATE PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES)Brandeis University Waltham, MA 02454 PERFORMING ORGANIZATION REPORT NUMBER SPONSORING / MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR/MONITOR'S ACRONYM(S) U.S. Army Medical Research and Materiel Command Fort Detrick, Maryland 21702-5012 SPONSOR/MONITOR'S REPORT NUMBER(S) DISTRIBUTION / AVAILABILITY STATEMENTApproved for Public Release; Distribution Unlimited SUPPLEMENTARY NOTES ABSTRACTWork on sleep at Brandeis focuses on Drosophila melanogaster as well as the more traditional rodent models. The Drosophila works aims to exploit the genetic advantages of this organism yet still learn about aspects of sleep relevant to humans. The major finding has been that the human therapeutic Carbamazapine is a potent sleep-deprivation agent in flies. Current data indicate that its effects are mediated through the Rdl GABAA receptor, which has implications for the role of this drug in humans. One of the rodent laboratories is focused on the regulation of sleep and waking in the basal forebrain. The goal is to identify gene expression changes in its cholinergic neuronal subset, and specific neuron purification has been accomplished. Another rodent laboratory is studying the effects of sleep deprivation on the intrinsic electrophysiology and gene expression properties of neocortical neurons. Interesting changes in firing properties of layer 5 pyramidal neurons have been observed, and gene expression assays from these cells are underway. The final two projects involve the role of sleep in homeostatic plasticity and fear conditioning. These are being done both in vivo, in freely behaving animals, and "ex vivo, in cortical slices after sleep deprivation or training. SUBJECT TERMSSleep, Learning, Gene Regulation, Neuron Plasticity General IntroductionThere were eight PIs over the past few years at Brandeis with a common interest in sleep. During the past few years, Dr. Katz's (Aim 6) research interests have lead away from sleep leaving seven labs dedicated to sleep investigation. Although the investigators run autonomous research programs with individual reports, ev...

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A hierarchical algorithm for calculating the isotopic fine structures of molecules

Cited by 27 publications

References 28 publications

An Efficient Method to Calculate the Aggregated Isotopic Distribution and Exact Center-Masses

An Efficient Method to Calculate the Aggregated Isotopic Distribution and Exact Center-Masses

Drought and Recovery: Independently Regulated Processes Highlighting the Importance of Protein Turnover Dynamics and Translational Regulation in Medicago truncatula

Functions and Mechanisms of Sleep in Flies and Mammals

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