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Protocols

Isotope Pattern Calculator specifications

Information


Unique identifier OMICS_02414
Name Isotope Pattern Calculator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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No version available

Isotope Pattern Calculator citations

 (6)
library_books

Determination of true ratios of different N glycan structures in electrospray ionization mass spectrometry

2017
Anal Bioanal Chem
PMCID: 5359385
PMID: 28271226
DOI: 10.1007/s00216-017-0235-8

[…] n was performed with an ESI calibration mixture (Agilent).Data interpretation was done with DataAnalysis 4.0 (Bruker, Bremen, Germany). Theoretical isotopic distributions were calculated with Compass isotope pattern calculator (Bruker, Bremen, Germany). For quantification with the “all peaks” strategy, the four (Man5) to seven (G4S4F) highest isotopic peaks (resulting in at least 96.5% of the over […]

library_books

Differential Molecular Responses of Rapeseed Cotyledons to Light and Dark Reveal Metabolic Adaptations toward Autotrophy Establishment

2016
Front Plant Sci
PMCID: 4944393
PMID: 27471506
DOI: 10.3389/fpls.2016.00988

[…] r-defined search parameters as described by . The false discovery rate (FDR) thresholds for protein and peptide were specified at 1%, and those with confidence levels higher than 95% were considered. Isotope pattern calculator was implemented to quantify the relative intensities of isotope peaks with ParagonTM Algorithm. The mass spectrometry proteomics data have been deposited in the ProteomeXcha […]

library_books

Software LS MIDA for efficient mass isotopomer distribution analysis in metabolic modelling

2013
BMC Bioinformatics
PMCID: 3720290
PMID: 23837681
DOI: 10.1186/1471-2105-14-218

[…] are [], Gepasi [] or FiatFlux [] (here fluxes are predicted after the isotopologue data have been processed). There are two software solutions available for isotopomer data processing, Envelop [] and Isotope Pattern Calculator [], but none uses binomial expression for data extension. The implementation of Brauman’s least square method with the inclusion of binomial expression allows rapid and accu […]

call_split

A six plex proteome quantification strategy reveals the dynamics of protein turnover

2013
Sci Rep
PMCID: 3650664
PMID: 23661174
DOI: 10.1038/srep01827
call_split See protocol

[…] ic cluster. Therefore for each isotopic label form the first four peaks were used for calculated the intensity. The influence of overlapped isotope clusters was also considered. A software tool named Isotope Pattern Calculator (IPC) download from http://omics.pnl.gov/software/IPC.php was used to calculate the relative intensities of isotope peaks and the overlapped portion were deducted. In a MS1 […]

library_books

Hydrodynamic properties of cyclodextrin molecules in dilute solutions

2009
Eur Biophys J
PMCID: 2812710
PMID: 19159925
DOI: 10.1007/s00249-008-0394-9

[…] ach measurement with an external PMMA standard from PSS Polymer Standards Services GmbH (Mainz, Germany) in the required measurement range. MS and MS/MS data were processed using PolyTools 1.0 and an isotope pattern calculator. […]

library_books

Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis

2007
BMC Syst Biol
PMCID: 1839890
PMID: 17408502
DOI: 10.1186/1752-0509-1-12

[…] atabases. The isotopic distribution is based on observed natural abundance of each element in the chemical formula []. Isotopic masses and abundances of given chemical composition are predicted using Isotope Pattern Calculator version 1.4 []. While the exact isotope patterns are kept in the database, the patterns are corrected for resolution of the mass spectrometer when matching with spectral dat […]


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