Label-free relative quantification of co-eluting isobaric phosphopeptides of insulin receptor substrate-1 by HPLC-ESI-MS/MS

Intracellular signal transduction is often regulated by transient protein phosphorylation in response to external stimuli. Insulin signaling is dependent on specific protein phosphorylation events, and analysis of insulin receptor substrate-1 (IRS-1) phosphorylation reveals a complex interplay between tyrosine, serine, and threonine phosphorylation. The phosphospecific antibody-based quantification approach for analyzing changes in site-specific phosphorylation of IRS-1 is difficult due to the dearth of phospho-antibodies compared with the large number of known IRS-1 phosphorylation sites. We previously published a method detailing a peak area-based mass spectrometry approach, using precursor ions for peptides, to quantify the relative abundance of site-specific phosphorylation in the absence or presence of insulin. We now present an improvement wherein site-specific phosphorylation is quantified by determining the peak area of fragment ions respective to the phospho-site of interest. This provides the advantage of being able to quantify co-eluting isobaric phosphopeptides (differentially phosphorylated versions of the same peptide), allowing for a more comprehensive analysis of protein phosphorylation. Quantifying human IRS-1 phosphorylation sites at Ser303, Ser323, Ser330, Ser348, Ser527, and Ser531 shows that this method is linear (n = 3; r² = 0.85 ± 0.05, 0.96 ± 0.01, 0.96 ± 0.02, 0.86 ± 0.07, 0.90 ± 0.03, 0.91 ± 0.04, respectively) over an approximate 10-fold range of concentrations and reproducible (n = 4; coefficient of variation = 0.12, 0.14, 0.29, 0.30, 0.12, 0.06, respectively). This application of label-free, fragment ion-based quantification to assess relative phosphorylation changes of specific proteins will prove useful for understanding how various cell stimuli regulate protein function by phosphorylation.     

Green Approaches to Field Nitrate Analysis: An Electroanalytical Perspective

The different approaches that have been taken in the development of analytical methods for the determination of nitrate within the field are reviewed. The emphasis has been placed on providing a critical appraisal of the chemistry that underpins current commercial systems and the need to remove the dependence on heavy metal and concentrated acid components. The search for more environmentally acceptable and user friendly systems has long been pursued and the present communication seeks to explore the recent development in portable testing technologies and how they might evolve in the future. In particular, the role of electrochemical techniques in the latter are investigated and their potential application compared and contrasted with the more traditional wet chemical detection strategies.     

Report of an IEEE Task Force?An IEEE Opinion on Research Needs for Biomedical Engineerng Systems

MORE than 200 years ago, our forefathers made note of man's inalienable rights to life, liberty, and the pursuit of happiness. To the engineering community (applied science in the service of man), these may be coincident with applications to medicine and biology (biomedical engineering), defense, and entertainment. Biomedical engineering research has the distinction, among these three missions, of not only contributing to the quality of human life through the industrial economy but also to life itself?the most fundamental concern of all people. It is through biomedical engineering research that we have been able to learn much concerning the functioning of living systems, and it is through such knowledge that we have been able to develop improved clinical diagnosis, monitoring, and treatment, including life-sustaining devices and aids to the handicapped. Each step represents an improvement in the quality of life, and each step forms the foundation upon which to gain new knowledge to improve upon earlier developments.     

Extending the GGobi pipeline from R

This paper describes progress towards developing a platform for rapid prototyping of interactive data visualizations, using R, GGobi, rggobi and RGtk2. GGobi is a software tool for multivariate interactive graphics. At the core of GGobi is a data pipeline that incrementally transforms data through a series of stages into a plot and maps user interaction with the plot back to the data. The GGobi pipeline is extensible and mutable at runtime. The rggobi package, an interface from the R language to GGobi, has been augmented with a low-level interface that supports the customization of interactive data visualizations through the extension and manipulation of the GGobi pipeline. The large size of the GGobi API has motivated the use of the RGtk2 code generation system to create the low-level interface between R and GGobi. The software is demonstrated through an application to interactive network visualization.