Algorithm 676: ODRPACK: software for weighted orthogonal distance regression

Boggs, Paul T.; Donaldson, Janet R.; Byrd, Richard H.; Schnabel, Robert B.

doi:10.1145/76909.76913

Cited by 281 publications

(252 citation statements)

References 9 publications

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“…The uncertainties were calculated by weight orthogonal distance regression (ODR) using the ODRPAC suite of program [86]. The uncertainties were calculated by weight orthogonal distance regression (ODR) using the ODRPAC suite of program [86].…”

Section: Discussionmentioning

confidence: 99%

Gas-phase acidities of cysteine-polyglycine peptides: The effect of the cysteine position

Morishetti

Huang

Yates

et al. 2010

J. Am. Soc. Mass Spectrom.

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The sequence and conformational effects on the gas-phase acidities of peptides have been studied by using two pairs of isomeric cysteine-polyglycine peptides, CysGly 3,4 NH 2 and Gly 3,4 CysNH 2 . The extended Cooks kinetic method was employed to determine the gas-phase acidities using a triple quadrupole mass spectrometer with an electrospray ionization source. The ion activation was achieved via collision-induced dissociation experiments. The deprotonation enthalpies (⌬ acid H) were determined to be 323.9 Ϯ 2.5 kcal/mol (CysGly 3 NH 2 ), 319.2 Ϯ 2.3 kcal/mol (CysGly 4 NH 2 ), 333.8 Ϯ 2.1 kcal/mol (Gly 3 CysNH 2 ), and 321.9 Ϯ 2.8 kcal/mol (Gly 4 CysNH 2 ), respectively. The corresponding deprotonation entropies (⌬ acid S) of the peptides were estimated. The gas-phase acidities (⌬ acid G) were derived to be 318.4 Ϯ 2.5 kcal/mol (CysGly 3 NH 2 ), 314.9 Ϯ 2.3 kcal/mol (CysGly 4 NH 2 ), 327.5 Ϯ 2.1 kcal/mol (Gly 3 CysNH 2 ), and 317.4 Ϯ 2.8 kcal/mol (Gly 4 CysNH 2 ), respectively. Conformations and energetic information of the neutral and anionic peptides were calculated through simulated annealing (Tripos), geometry optimization (AM1), and single point energy calculations (B3LYP/6-31ϩG(d)), respectively. Both neutral and deprotonated peptides adopt many possible conformations of similar energies. All neutral peptides are mainly random coils. The two C-cysteine anionic peptides, Gly 3,4 (Cys-H) Ϫ NH 2 , are also random coils. The two N-cysteine anionic peptides, (Cys-H) Ϫ Gly 3,4 NH 2 , may exist in both random coils and stretched helices. The two N-cysteine peptides, CysGly 3 NH 2 and CysGly 4 NH 2 , are significantly more acidic than the corresponding C-terminal cysteine ones, Gly 3 CysNH 2 and Gly 4 CysNH 2 . The stronger acidities of the former may come from the greater stability of the thiolate anion resulting from the interaction with the helix-macrodipole, in addition to the hydrogen bonding interactions. (J Am Soc Mass Spectrom 2010, 21, 603-614)

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Section: Discussionmentioning

confidence: 99%

Gas-phase acidities of cysteine-polyglycine peptides: The effect of the cysteine position

Morishetti

Huang

Yates

et al. 2010

J. Am. Soc. Mass Spectrom.

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“…Internal calibration was performed using eq 2 after all calibration coefficients were fit using a LevenbergMarquardt algorithm [60] for each mass spectrum acquired during the LC separation. The frequencies of calibrant ions from adjacent scans were used with weight coefficients to provide higher statistical confidence.…”

Section: Capillary Lc-fticr Analysesmentioning

confidence: 99%

An automated high performance capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics

Belov

Anderson

Wingerd

et al. 2004

J. Am. Soc. Mass Spectrom.

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We describe a fully automated high performance liquid chromatography 9.4 tesla Fourier transform ion resonance cyclotron (FTICR) mass spectrometer system designed for proteomics research. A synergistic suite of ion introduction and manipulation technologies were developed and integrated as a high-performance front-end to a commercial Bruker Daltonics FTICR instrument. The developments incorporated included a dual-ESI-emitter ion source; a dualchannel electrodynamic ion funnel; tandem quadrupoles for collisional cooling and focusing, ion selection, and ion accumulation, and served to significantly improve the sensitivity, dynamic range, and mass measurement accuracy of the mass spectrometer. In addition, a novel technique for accumulating ions in the ICR cell was developed that improved both resolution and mass measurement accuracy. A new calibration methodology is also described where calibrant ions are introduced and controlled via a separate channel of the dual-channel ion funnel, allowing calibrant species to be introduced to sample spectra on a real-time basis, if needed. We also report on overall instrument automation developments that facilitate high-throughput and unattended operation. These included an automated version of the previously reported very high resolution, high pressure reversed phase gradient capillary liquid chromatography (LC) system as the separations component. A commercial autosampler was integrated to facilitate 24 h/day operation. Unattended operation of the instrument revealed exceptional overall performance: Reproducibility (1-5% deviation in uncorrected elution times), repeatability (Ͻ20% deviation in detected abundances for more abundant peptides from the same aliquot analyzed a few weeks apart), and robustness (high-throughput operation for 5 months without significant downtime). When combined with modulated-ionenergy gated trapping, the dynamic calibration of FTICR mass spectra provided decreased mass measurement errors for peptide identifications in conjunction with high resolution capillary LC separations over a dynamic range of peptide peak intensities for each spectrum of 10 3 , and Ͼ10 5 for peptide abundances in the overall separation. (J Am Soc Mass Spectrom 2004, 15, 212-232)

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“…Eqs. (9)- (18) were solved using the ODRPACK package [22] with the ordinary least squares criterion. Re-parameterization was performed on k D and E a being the estimated parameters β 1 = ln (k D ) − E a /300R and β 2 = E a /300R.…”

Section: Resultsmentioning

confidence: 99%

Heterogeneous studies in pulping of wood: Modelling mass transfer of alkali

Simão

Egas

Carvalho

et al. 2008

Chemical Engineering Journal

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In this paper a heterogeneous lumped parameter model is proposed to describe the mass transfer of effective alkali during the kraft pulping of wood. This model, based on the spatial mean of the concentration profile of effective alkali along the chip thickness, enables the estimation of the effective diffusion coefficient that characterizes the internal resistance to mass transfer and the contribution of the external resistance to mass transfer which has often been neglected.The experimental data that support this study comprise measurements of alkali concentration in the liquid phases, both inside and outside the chips. The kraft pulping of Eucalyptus globulus was carried out using broad range of temperature (80-165 • C) and effective alkali charge (10-45 g Na 2 O (100 g odw) −1 ).The model describes the effective alkali concentration profiles in the free liquor along the cooking with accuracy. The effective diffusion coefficient has been expressed by an Arrhenius-type equation and the estimated value of the activation energy for diffusion (E a = 20.7 kJ mol −1 ) is in agreement with previous studies. The contribution of the external resistance to the overall mass transfer resistance showed to be significant and to increase with both temperature and effective alkali charge at industrial operation conditions. This result confirms the relevance of building a model that takes into account the heterogeneous nature of the kraft pulping of E. globulus.

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Algorithm 676: ODRPACK: software for weighted orthogonal distance regression

Cited by 281 publications

References 9 publications

Gas-phase acidities of cysteine-polyglycine peptides: The effect of the cysteine position

Gas-phase acidities of cysteine-polyglycine peptides: The effect of the cysteine position

An automated high performance capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics

Heterogeneous studies in pulping of wood: Modelling mass transfer of alkali

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