Approaching complete peroxisome characterization by gas-phase fractionation

Yi, Eugene C.; Marelli, Marcello; Lee, Hookeun; Purvine, Samuel O.; Aebersold, Ruedi; Aitchison, John D.; Goodlett, David R.

doi:10.1002/1522-2683(200209)23:18<3205::aid-elps3205>3.0.co;2-y

Cited by 192 publications

(184 citation statements)

References 40 publications

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Section: Introductionsupporting

confidence: 71%

“…We show that the combination of zoom scan data acquisition and analysis using ZoomQuant provides calculation of isotopic ratios accurate to ~21%. This compares well with data produced from 18 O labeling experiments using time of flight (TOF) and Fourier transform-ion cyclotron resonance (FT-ICR) MS instruments.There is a growing impetus to develop methods for relative quantification of proteins and peptides that are compatible with shotgun methods and high throughput experiments. Two general approaches have thus far been used.…”

supporting

confidence: 71%

“…

AbstractStable isotope labeling with 18 O is a promising technique for obtaining both qualitative and quantitative information from a single differential protein expression experiment. The small 4 Da mass shift produced by incorporation of two molecules of 18 O, and the lack of available methods for automated quantification of large data sets has limited the use of this approach with electrospray ionization-ion trap (ESI-IT) mass spectrometers.

…”

mentioning

confidence: 99%

“…The use of zoom scans does potentially decrease the number of peptides that can be identified from a single chromatographic peak. However, extended gradients and gas phase fractionation [18,19] with replicate runs can be used to offset this limitation. Newly developed linear trap instruments offer much higher scan speeds and sensitivity.…”

mentioning

confidence: 99%

“…Isotopic labeling with 18 O provides an alternative method for obtaining quantitative information that offers many advantages to the methods described above. Every peptide in a peptide mixture is labeled through the enzyme mediated oxygen substitution (EMOS) [8] of serine proteases, with the exception of carboxy-terminal peptides [9].…”

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confidence: 99%

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Simultaneous quantification and identification using ¹⁸O labeling with an ion trap mass spectrometer and the analysis software application “ZoomQuant”

Hicks

Halligan

Slyper

et al. 2005

J. Am. Soc. Mass Spectrom.

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Stable isotope labeling with 18 O is a promising technique for obtaining both qualitative and quantitative information from a single differential protein expression experiment. The small 4 Da mass shift produced by incorporation of two molecules of 18 O, and the lack of available methods for automated quantification of large data sets has limited the use of this approach with electrospray ionization-ion trap (ESI-IT) mass spectrometers. In this paper, we describe a method of acquiring ESI-IT mass spectrometric data that provides accurate calculation of relative ratios of peptides that have been differentially labeled using 18 O. The method utilizes zoom scans to provide high resolution data. This allows for accurate calculation of 18 O/ 16 O ratios for peptides even when as much as 50% of a 18 O labeled peptide is present as the singly labeled species. The use of zoom scan data also provides sufficient resolution for calculating accurate ratios for peptides of +3 and lower charge states. Sequence coverage is comparable to that obtained with data acquisition modes that use only MS and MS/MS scans. We have employed a newly developed analysis software tool, ZoomQuant, which allows for the automated analysis of large data sets. We show that the combination of zoom scan data acquisition and analysis using ZoomQuant provides calculation of isotopic ratios accurate to ~21%. This compares well with data produced from 18 O labeling experiments using time of flight (TOF) and Fourier transform-ion cyclotron resonance (FT-ICR) MS instruments.There is a growing impetus to develop methods for relative quantification of proteins and peptides that are compatible with shotgun methods and high throughput experiments. Two general approaches have thus far been used. Both approaches depend on the use of "light" and "heavy" isotopes to differentially label proteins from two different populations of cells grown under variant conditions. The resultant mass shift provides a mass based separation for otherwise identical molecules from both cell populations that can be used for relative quantification. In-vivo labeling methods, such as metabolic labeling relying on the incorporation of isotopically labeled specific amino acids [1], or complete substitution of 14 N with 15 N [2], cannot be used for many mammalian systems. Yates et al. have reported success with in-vivo metabolic labeling of rat proteins by providing them with a diet enriched in 15 N labeled amino acids [3]. Post-translational methods of labeling are applicable to eukaryotic systems. These methods introduce mass shifts through the modification of the side chains of specific amino acids, such lysine [4] and cysteine [5], labeling of the carboxy, or amino terminus of peptides. Isotope-coded affinity tag (ICAT), which introduces "heavy" and "light" variants of an affinity tag that modifies cysteines, is the most well developed technology for post translational modification of peptides for differential protein expression analysis b y mass Experimental ChemicalsEquine s...

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Section: Introductionsupporting

confidence: 71%

supporting

confidence: 71%

“…

…”

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Simultaneous quantification and identification using ¹⁸O labeling with an ion trap mass spectrometer and the analysis software application “ZoomQuant”

Hicks

Halligan

Slyper

et al. 2005

J. Am. Soc. Mass Spectrom.

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Quantitative Protein Profile Comparisons Using the Isotope‐Coded Affinity Tag Method

2003

CP Protein Science

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Current methods for measuring pairwise changes in protein expression involve differential stable isotopic labeling of proteins or peptides either in vivo or in vitro followed by identification and quantification using a mass spectrometer. In these methods, the mass spectrometer detects two different masses, which correspond to a single protein from two different samples that have been labeled with either a heavy or normal isotope. Changes in protein expression are observed when the identical peptide from each of two biological conditions is identified and a difference is detected in the measurements comparing the peptide labeled with the heavy isotope to the one with a normal isotopic distribution. This approach allows the simultaneous comparison of the expression of many proteins between two different biological states (e.g., yeast grown on galactose versus glucose, or normal versus cancer cells). This unit describes one of these popular methods for quantitative protein profiling using the isotope-coded affinity tag (ICAT) technique.

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The Isotope‐Coded Affinity Tag Method for Quantitative Protein Profile Comparison and Relative Quantitation of Cysteine Redox Modifications

2015

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The isotope-coded affinity tag (ICAT) technique has been applied to measure pairwise changes in protein expression through differential stable isotopic labeling of proteins or peptides followed by identification and quantification using a mass spectrometer. Changes in protein expression are observed when the identical peptide from each of two biological conditions is identified and a difference is detected in the measurements comparing the peptide labeled with the heavy isotope to the one with a normal isotopic distribution. This approach allows the simultaneous comparison of the expression of many proteins between two different biological states (e.g., yeast grown on galactose versus glucose, or normal versus cancer cells). Due to the cysteine-specificity of the ICAT reagents, the ICAT technique has also been applied to perform relative quantitation of cysteine redox modifications such as oxidation and nitrosylation. This unit describes both protein quantitation and profiling of cysteine redox modifications using the ICAT technique.

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Approaching complete peroxisome characterization by gas-phase fractionation

Cited by 192 publications

References 40 publications

Simultaneous quantification and identification using ¹⁸O labeling with an ion trap mass spectrometer and the analysis software application “ZoomQuant”

Simultaneous quantification and identification using ¹⁸O labeling with an ion trap mass spectrometer and the analysis software application “ZoomQuant”

Quantitative Protein Profile Comparisons Using the Isotope‐Coded Affinity Tag Method

The Isotope‐Coded Affinity Tag Method for Quantitative Protein Profile Comparison and Relative Quantitation of Cysteine Redox Modifications

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Approaching complete peroxisome characterization by gas-phase fractionation

Cited by 192 publications

References 40 publications

Simultaneous quantification and identification using 18O labeling with an ion trap mass spectrometer and the analysis software application “ZoomQuant”

Simultaneous quantification and identification using 18O labeling with an ion trap mass spectrometer and the analysis software application “ZoomQuant”

Quantitative Protein Profile Comparisons Using the Isotope‐Coded Affinity Tag Method

The Isotope‐Coded Affinity Tag Method for Quantitative Protein Profile Comparison and Relative Quantitation of Cysteine Redox Modifications

Contact Info

Product

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About

Simultaneous quantification and identification using ¹⁸O labeling with an ion trap mass spectrometer and the analysis software application “ZoomQuant”

Simultaneous quantification and identification using ¹⁸O labeling with an ion trap mass spectrometer and the analysis software application “ZoomQuant”