Mass spectrometry-based quantitative proteomics has become an important component of biological and clinical research. Although such analyses typically assume that a protein's peptide fragments are observed with equal likelihood, only a few so-called 'proteotypic' peptides are repeatedly and consistently identified for any given protein present in a mixture. Using >600,000 peptide identifications generated by four proteomic platforms, we empirically identified >16,000 proteotypic peptides for 4,030 distinct yeast proteins. Characteristic physicochemical properties of these peptides were used to develop a computational tool that can predict proteotypic peptides for any protein from any organism, for a given platform, with >85% cumulative accuracy. Possible applications of proteotypic peptides include validation of protein identifications, absolute quantification of proteins, annotation of coding sequences in genomes, and characterization of the physical principles governing key elements of mass spectrometric workflows (e.g., digestion, chromatography, ionization and fragmentation).

Aberrant interactions between the host and the intestinal bacteria are thought to contribute to the pathogenesis of many digestive diseases. However, studying the complex ecosystem at the human mucosal-luminal interface (MLI) is challenging and requires an integrative systems biology approach. Therefore, we developed a novel method integrating lavage sampling of the human mucosal surface, high-throughput proteomics, and a unique suite of bioinformatic and statistical analyses. Shotgun proteomic analysis of secreted proteins recovered from the MLI confirmed the presence of both human and bacterial components. To profile the MLI metaproteome, we collected 205 mucosal lavage samples from 38 healthy subjects, and subjected them to high-throughput proteomics. The spectral data were subjected to a rigorous data processing pipeline to optimize suitability for quantitation and analysis, and then were evaluated using a set of biostatistical tools. Compared to the mucosal transcriptome, the MLI metaproteome was enriched for extracellular proteins involved in response to stimulus and immune system processes. Analysis of the metaproteome revealed significant individual-related as well as anatomic region-related (biogeographic) features. Quantitative shotgun proteomics established the identity and confirmed the biogeographic association of 49 proteins (including 3 functional protein networks) demarcating the proximal and distal colon. This robust and integrated proteomic approach is thus effective for identifying functional features of the human mucosal ecosystem, and a fresh understanding of the basic biology and disease processes at the MLI.

In subtypes and late stages of leukemias driven by the tyrosine kinase fusion protein Bcr-Abl, Src signaling critically contributes to the leukemic phenotype. We performed global tyrosine phosphoprofiling using quantitative mass spectrometry of Bcr-Abl transformed cells in which the activities of the Src family kinases (SFKs) were perturbed to build a detailed context-dependent network of cancer signaling. Perturbation of the SFKs Lyn and Hck with genetics or inhibitors revealed Bcr-Abl downstream phosphorylation events either mediated by or independent of SFKs. We identified multiple negative feedback mechanisms within the network of signaling events affected by Bcr-Abl and SFKs, and found that Bcr-Abl attenuated these inhibitory mechanisms. The Csk binding protein Pag1 (also known as Cbp) and the tyrosine phosphatase Ptpn18 both mediated negative feedback to SFKs. We observed Bcr-Abl-mediated phosphorylation of the phosphatase Shp2 (Ptpn11) and this may contribute to the suppression of these negative feedback mechanisms to promote Bcr-Abl-activated SFK signaling. Csk and a kinase-deficient Csk mutant both produced similar globally repressive signaling consequences, suggesting a critical role for the adaptor protein function of Csk in its inhibition of Bcr-Abl and SFK signaling. The identified Bcr-Abl-activated SFK regulatory mechanisms are candidates for dysregulation during leukemia progression and acquisition of SFK-mediated drug resistance.

Previous studies have shown that oxidized products of the phospholipid PAPC (Ox-PAPC) are strong activators of aortic endothelial cells and play an important role in atherosclerosis and other inflammatory diseases. We and others have demonstrated that Ox-PAPC activates specific signaling pathways and regulates a large number of genes. Using a phosphoproteomic approach based on phosphopeptide enrichment and mass spectrometry analysis, we identified candidate changes in Ox-PAPC-induced protein phosphorylation of 228 proteins. Functional annotation of these proteins showed an enrichment of the regulation of cytoskeleton, junctional components, and tyrosine kinases, all of which may contribute to the phenotypic and molecular changes observed in endothelial cells treated with Ox-PAPC. Many changes in protein phosphorylation induced by Ox-PAPC are reported here for the first time and provide new insights into the mechanism of activation by oxidized lipids, including phosphorylation-based signal transduction.

The goal of quantitative proteomics is to determine the identity and relative quantity of each protein present in two or more complex protein samples. Here we describe a novel approach to quantitative proteomics. It is based on a highly accurate algorithm for the automated quantification of chromatographically fractionated, isotope-coded affinity-tagged peptides and MALDI quadrupole time-of-flight tandem mass spectrometry for their identification. The method is capable of detecting and selectively identifying those proteins within a complex mixture that show a difference in relative abundance. We demonstrate the effectiveness and the versatility of this approach in the analysis of a standard protein mixture, protein expression profiling in a human prostate cancer cell line model, and identification of the specific components of the multiprotein transcriptional machinery in S. cerevisiae.

Particularly in hot climates, various pigments are used to formulate desired non-white colors that stay cooler in the sun than alternatives. These cool pigments provide a high nearinfrared (NIR) reflectance in the solar infrared range of 700 to 2500 nm, and also a color specified by a reflectance spectrum in the 400 to 700 nm visible range. Still cooler materials can be formulated by also utilizing the phenomenon of fluorescence (photoluminescence). Ruby, Al 2 O 3 :Cr, is a prime example, with efficient emission in the deep red (~694 nm) and near infrared (700-800 nm). A layer of synthetic ruby crystals on a white surface having an attractive red color can remain cooler in the sun than conventional red materials. Ruby particles can also be used as a red/pink pigment. Increasing the Cr:Al ratio produces a stronger (darker) pigment but doping above ~3 wt % Cr 2 O 3 causes concentration quenching of the fluorescence. The system quantum efficiency for lightly doped ruby-pigmented coatings over white is high, 0.83 ± 0.10.

The alkaline earth copper tetra-silicates, blue pigments, are interesting infrared phosphors. The Ca, Sr, and Ba variants fluoresce in the near-infrared (NIR) at 909, 914, and 948 nm, respectively, with spectral widths on the order of 120 nm. The highest quantum yield / reported thus far is ca. 10%. We use temperature measurements in sunlight to determine this parameter. The yield depends on the pigment loading (mass per unit area) x with values approaching 100% as x ! 0 for the Ca and Sr variants. Although maximum quantum yield occurs near x ¼ 0, maximum fluorescence occurs near x ¼ 70 g m À2 , at which / ¼ 0.7. The better samples show fluorescence decay times in the range of 130 to 160 ls. The absorbing impurity CuO is often present. Good phosphor performance requires long fluorescence decay times and very low levels of parasitic absorption. The strong fluorescence enhances prospects for energy applications such as cooling of sunlit surfaces (to reduce air conditioning requirements) and luminescent solar concentrators.

Dry anaerobic digestion (AD) of organic municipal solid waste (MSW) followed by composting of the residual digestate is a waste diversion strategy that generates biogas and soil amendment products. The AD-composting process avoids methane (CH4) emissions from landfilling, but emissions of other greenhouse gases, odorous/toxic species, and reactive compounds can affect net climate and air quality impacts. In situ measurements of key sources at two large-scale industrial facilities in California were conducted to quantify pollutant emission rates across the AD-composting process. These measurements established a strong relationship between flared biogas ammonia (NH3) content and emitted nitrogen oxides (NO x ), indicating that fuel NO x formation is significant and dominates over the thermal or prompt NO x pathways when biogas NH3 concentration exceeds ∼200 ppm. Composting is the largest source of CH4, carbon dioxide (CO2), nitrous oxide (N2O), and carbon monoxide (CO) emissions (∼60–70%), and dominate NH3, hydrogen sulfide (H2S), and volatile organic compounds (VOC) emissions (>90%). The high CH4 contribution to CO2-equivalent emissions demonstrates that composting can be an important CH4 source, which could be reduced with improved aeration. Controlling greenhouse gas and toxic/odorous emissions from composting offers the greatest mitigation opportunities for reducing the climate and air quality impacts of the AD-composting process.