The Oscillation Numbers and the Abramov Method of Spectral Counting for Linear Hamiltonian Systems

In this paper we consider linear Hamiltonian differential systems which depend in general nonlinearly on the spectral parameter and with Dirichlet boundary conditions. For the Hamiltonian problems we do not assume any controllability and strict normality assumptions which guarantee that the classical eigenvalues of the problems are isolated. We also omit the Legendre condition for their Hamiltonians. We show that the Abramov method of spectral counting can be modified for the more general case of finite eigenvalues of the Hamiltonian problems and then the constructive ideas of the Abramov method can be used for stable calculations of the oscillation numbers and finite eigenvalues of the Hamiltonian problems.

Improved LC-MS chromatographic alignment increases the accuracy of label-free quantitative proteomics: Comparison of spectral counting versus ion intensity-based proteomic quantification strategies

The ability to provide an unbiased qualitative and quantitative description of the global changes to proteins in a cell or an organism would permit the systems-wide study of complex biological systems. Label-free quantitative shotgun proteomic strategies (including LC-MS ion intensity quantification and spectral counting) are attractive because of their relatively low cost, ease of implementation, and the lack of multiplexing restrictions when comparing multiple samples. Owing to improvements in the resolution and sensitivity of mass spectrometers, and the availability of analytical software packages, protein quantification by LC-MS ion intensity has increased in popularity. Here, we have addressed the importance of chromatographic alignment on protein quantification, and then assessed how spectral counting compares to ion intensity-based proteomic quantification. Using a spiked-in protein strategy, we analysed two situations that commonly arise in the application of proteomics to cell biology: (i) samples with a small number of proteins of differential abundance in a larger non-changing background, and (ii) samples with a larger number of proteins of differential abundance. To perform these assessments on biologically relevant samples, we used isolated integrin adhesion complexes (IACs). Technical replicate analysis of isolated IACs resulted in a range of alignment scores using the Progenesis QI software package and demonstrated that higher LC-MS chromatographic alignment scores increased the precision of protein quantification. Furthermore, implementation of a simple sample batch-running strategy enabled good chromatographic alignment for hundreds of samples over multiple batches. Finally, we applied the sample batch-running strategy and compared quantification by LC-MS ion intensity to spectral counting and found that quantification by LC-MS ion intensity was more accurate and precise. In summary, these results demonstrate that chromatographic alignment is important for precise and accurate protein quantification based on LC-MS ion intensity and accordingly we present a simple sample re-ordering strategy to facilitate improved alignment. These findings are not only relevant to label-free quantification using Progenesis QI but may be useful to the wide range of MS-based quantification strategies that rely on chromatographic alignment.

Abstract 16404: CETP Inhibitor K-312 Lowers PCSK9 Expression and LDL Cholesterol Levels in vivo

Background: Despite potent LDL-cholesterol (LDL-C) therapies, substantial residual cardiovascular risk remains. Proprotein convertase subtilisin/kexin 9 (PCSK9) is a promising target for lowering LDL-C. We recently demonstrated that K-312, originally found as a cholesteryl ester transfer protein (CETP) inhibitor, decreased PCSK9 expression in vitro through the reduction of its promoter activity. The present study has further examined the underlying molecular mechanisms and in vivo effects of K-312 on PCSK9 levels using mass spectrometry. Methods and Results: CETP silencing by siRNA in the human hepatocyte cell line HepG2 did not compromise suppression of PCSK9 expression by K-312, indicating a mechanism independent of CETP inhibition. Transcription factors sterol-regulatory element binding protein (SREBP)-1 and SREBP-2 bind to the sterol regulatory element (SRE) of PCSK9 promoter when their precursor forms are cleaved into active forms. K-312 treatment decreased binding of SREBP-1 and SREBP-2 to SRE of the PCSK9 promoter (chromatin immunoprecipitation) and active forms of SREBP-1 and SREBP-2 (western blotting), suggesting the suppression of PCSK9 expression by K-312 involves SREBP-1 and SREBP-2. We then examined the effects of K-312 in cholesterol-fed New Zealand White rabbits administered either vehicle (N=7) or K-312 30 mg/kg (N=7) for 2 weeks. K-312 treatment decreased LDL-C (vehicle: 272.5 ± 42.2 mg/dl; K-312: 193.0 ± 36.5 mg/dl), increased HDL cholesterol (vehicle: 29.9 ± 3.7 mg/dl; K-312: 93.3 ± 14.7 mg/dl) and decreased PCSK9 mRNA levels in the liver by 63%. We further used two mass spectrometry-based approaches to measure PCSK9 levels in rabbit plasma: spectral counting and a novel high resolution (HR)-MS/MS quantification method. Immunoprecipitation of PCSK9 successfully enriched PCSK9 signal. Spectral counting and HR-MS/MS of PCSK9 peptides both demonstrated that K-312 treatment significantly decreased plasma PCSK9 levels by 76% (p<0.01) and 60% (p<0.05), respectively. Conclusion: K-312 may lower LDL cholesterol levels by suppressing CETP activity and PCSK9 expression, serving as a novel therapy for dyslipidemia and cardiovascular disease.