Automated Broadband Phase Correction of Fourier Transform Ion Cyclotron Resonance Mass Spectra

Xian, Feng; Hendrickson, Christopher L.; Blakney, Greg T.; Beu, Steven C.; Marshall, Alan G.

doi:10.1021/ac101091w

Cited by 169 publications

(206 citation statements)

References 30 publications

Supporting

Mentioning

202

Contrasting

Order By: Relevance

“…The molecular mass of each peak was determined by deconvolution of multiply charged ion species and then compared with the calculated masses of all histone H2B sequence variants (Table I). All raw ECD product ion mass spectra were phase-corrected and analyzed by our in-house software in a variant-specific man-ner to determine each proteoform (55,56). Briefly, a library of all known H2B sequence variants from Uniprot was imported into our software for identification and characterization.…”

Section: Transformation Of Cells By Low-dose Chronic Exposure Tomentioning

confidence: 99%

Quantitative Mass Spectrometry Reveals Changes in Histone H2B Variants as Cells Undergo Inorganic Arsenic-Mediated Cellular Transformation

Rea

Eleazer

Eckstein

et al. 2016

Molecular & Cellular Proteomics

Self Cite

View full text Add to dashboard Cite

Exposure to inorganic arsenic, a ubiquitous environmental toxic metalloid, leads to carcinogenesis. However, the mechanism is unknown. Several studies have shown that inorganic arsenic exposure alters specific gene expression patterns, possibly through alterations in chromatin structure. While most studies on understanding the mechanism of chromatin-mediated gene regulation have focused on histone post-translational modifications, the role of histone variants remains largely unknown. Incorporation of histone variants alters the functional properties of chromatin. To understand the global dynamics of chromatin structure and function in arsenic-mediated carcinogenesis, analysis of the histone variants incorporated into the nucleosome and their covalent modifications is required. Here we report the first global mass spectrometric analysis of histone H2B variants as cells undergo arsenic-mediated epithelial to mesenchymal transition. We used electron capture dissociation-based top-down tandem mass spectrometry analysis validated with quantitative reverse transcription real-time polymerase chain reaction to identify changes in the expression levels of H2B variants in inorganic arsenic-mediated epithelial-mesenchymal transition. We identified changes in the expression levels of specific histone H2B variants in two cell types, which are dependent on dose and length of exposure of inorganic arsenic. In particular, we found increases in H2B variants H2B1H/1K/1C/1J/1O and H2B2E/2F, and significant decreases in H2B1N/1D/1B as cells undergo inorganic arsenic-mediated epithelial-mesenchymal transition. The analysis of these histone vari-

show abstract

Section: Transformation Of Cells By Low-dose Chronic Exposure Tomentioning

confidence: 99%

Quantitative Mass Spectrometry Reveals Changes in Histone H2B Variants as Cells Undergo Inorganic Arsenic-Mediated Cellular Transformation

Rea

Eleazer

Eckstein

et al. 2016

Molecular & Cellular Proteomics

Self Cite

View full text Add to dashboard Cite

show abstract

“…For FT-ICR, it was recently demonstrated that, because of linear frequency sweep excitation, Φ(ω) is a quadratic function [32,33]. Recovery of the absorption-mode spectrum from the complex spectrum requires the correct phase angle function, Φ(ω); see Eq.…”

Section: Spectral Phase and Frequency-sweep Excitationmentioning

confidence: 99%

Phase Correction of Fourier Transform Ion Cyclotron Resonance Mass Spectra Using MatLab

Thompson

Orden

et al. 2011

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

FT-ICR mass spectrometry has been limited to magnitude mode for almost 40 years due to the data processing methods used. However, it is well known that phase correction of the data can theoretically produce an absorption-mode spectrum with a mass-resolving power that is as much as twice as high as conventional magnitude mode, and that it also improves the quality of the peak shape. Temporally dispersed frequency sweep excitation followed by a time delay before detection results in a steep quadratic variation in the signal phase with frequency. Viewing this, it is possible to find the correct phase function by performing a quadratic least squares fit, modified by iterating through phase cycles until the correct quadratic function is found. Here, we present a robust manual method to rotate these signals mathematically and generate a "phased" absorption-mode spectrum. The method can, in principle, be automated. Baseline correction is also included to eliminate the accompanying baseline drift. The resulting experimental FT-ICR absorption-mode spectra exhibit a resolving power that is at least 50% higher than that of the magnitude mode.

show abstract

“…Individual time-domain transients (80 -200; 6.1 sec each) for each spectrum were signal averaged, apodized with a full-Hanning (magnitude mode) or half-Hanning (absorption mode) weight function, and zero-filled once, prior to fast Fourier transformation. [41,42] The time-signal did not dampen to zero during the acquisition period. Due to increased complexity at higher m/z, a broadband phase correction was applied to each mass spectrum to produce absorption-mode display with increased mass resolution.…”

Section: Ft-icr Msmentioning

confidence: 96%

“…Due to increased complexity at higher m/z, a broadband phase correction was applied to each mass spectrum to produce absorption-mode display with increased mass resolution. [42,43] …”

Section: Ft-icr Msmentioning

confidence: 99%

Comprehensive study of a heavy fuel oil spill : modeling and analytical approaches to understanding environmental weathering

Lemkau¹

2012

View full text Add to dashboard Cite

Driven by increasingly heavy oil reserves and more efficient refining technologies, use of heavy fuel oils for power generation is rising. Unlike other refined products and crude oils, a large portion of these heavy oils is undetectable using the traditional gas chromatography-based techniques on which oil spill science has been based. In the current study, samples collected after the 2007 M/V Cosco Busan heavy fuel oil spill (San Francisco, CA) were analyzed using gas chromatography (GC)-based techniques, numerical modeling and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to examine natural weathering of the oil over a one and a half year period. Traditional GC techniques detected variable evidence of evaporation/ dissolution, biodegradation and photodegradation. Petroleum hydrocarbon compounds smaller than ~n-C 16 were rapidly lost due to evaporation and dissolution. Significant biodegradation was not detected until one month post spill while photodegradation was only observed at one field site. To further examine the processes of evaporation and dissolution, samples were analyzed with comprehensive two-dimensional GC (GC×GC) and a physiochemical model developed to approximate quantitative apportionment of compounds lost to the atmosphere and water. Model results suggest temperature is the primary control of evaporation. Finally, to examine the prominent non-GC amenable component of the oil, samples were analyzed with FT-ICR MS. Results showed expected clustering of samples, with those samples collected sooner after the spill having the most compositional similarity to the unweathered oil. Analysis of dominant heteroatom classes within the oil showed losses of high molecular weight species and the formation of stable core structures with time. These results highlight the susceptibility to weathering of these higher molecular weight components, previously believed to be recalcitrant in the environment. Research findings indicate that environmental weathering results in removal or alteration of larger alkylated compounds as well as loss of lower molecular weight species through evaporation/dissolution, biodegradation and photodegradation, with a resultant fraction of stable compounds likely to remain in the environment years after the spill. This research demonstrates the advantages of combining multiple analytical and modeling approaches for a fuller understanding of oil spill chemistry. AcknowledgementsThere are so many people that have helped me -personally and scientifically-along this journey. First I would like to thank my advisor Chris Reddy. You have been an amazing mentor, pushing me, allowing me to grow as a scientist and never wavering in your encouragement and support. I appreciate your willingness to explore the world outside of science through your public outreach. Although you may be a scientific workaholic (a topic of debate), you have always been tolerant of those of us who are less so, and I thank you for that. I appreciate the many people and experiences you...

show abstract

Automated Broadband Phase Correction of Fourier Transform Ion Cyclotron Resonance Mass Spectra

Cited by 169 publications

References 30 publications

Quantitative Mass Spectrometry Reveals Changes in Histone H2B Variants as Cells Undergo Inorganic Arsenic-Mediated Cellular Transformation

Quantitative Mass Spectrometry Reveals Changes in Histone H2B Variants as Cells Undergo Inorganic Arsenic-Mediated Cellular Transformation

Phase Correction of Fourier Transform Ion Cyclotron Resonance Mass Spectra Using MatLab

Comprehensive study of a heavy fuel oil spill : modeling and analytical approaches to understanding environmental weathering

Contact Info

Product

Resources

About