Richard C. Baliban

Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database

Post-translational modifications (PTMs) broadly contribute to the recent explosion of proteomic data and possess a complexity surpassing that of protein design. PTMs are the chemical modification of a protein after its translation, and have wide effects broadening its range of functionality. Based on previous estimates, it is widely believed that more than half of proteins are glycoproteins. Whereas mutations can only occur once per position, different forms of post-translational modifications may occur in tandem. With the number and abundances of modifications constantly being discovered, there is no method to readily assess their relative levels. Here we report the relative abundances of each PTM found experimentally and putatively, from high-quality, manually curated, proteome-wide data, and show that at best, less than one-fifth of proteins are glycosylated. We make available to the academic community a continuously updated resource (http://selene.princeton.edu/PTMCuration) containing the statistics so scientists can assess “how many” of each PTM exists.

High Throughput Characterization of Combinatorial Histone Codes

We present a novel method utilizing “saltless” pH gradient weak cation exchange-hydrophilic interaction liquid chromatography directly coupled to electron transfer dissociation (ETD) mass spectrometry for the automated on-line high throughput characterization of hypermodified combinatorial histone codes. This technique, performed on a low resolution mass spectrometer, displays an improvement over existing methods with an ∼100-fold reduction in sample requirements and analysis time. The scheme presented is capable of identifying all of the major combinatorial histone codes present in a sample in a 2-h analysis. The large N-terminal histone peptides are eluted by the pH and organic solvent weak cation exchange-hydrophilic interaction liquid chromatography gradient and directly introduced via nanoelectrospray ionization into a benchtop linear quadrupole ion trap mass spectrometer equipped with ETD. Each polypeptide is sequenced, and the modification sites are identified by ETD fragmentation. The isobaric trimethyl and acetyl modifications are resolved chromatographically and confidently distinguished by the synthesis of mass spectrometric and chromatographic information. We demonstrate the utility of the method by complete characterization of human histone H3.2 and histone H4 from butyrate-treated cells, but it is generally applicable to the analysis of highly modified peptides. We find this methodology very useful for chromatographic separation of isomeric species that cannot be separated well by any other chromatographic means, leading to less complicated tandem mass spectra. The improved separation and increased sensitivity generated novel information about much less abundant forms. In this method demonstration we report over 200 H3.2 forms and 70 H4 forms, including forms not yet detected in human cells, such as the remarkably highly modified histone H3.2 K4me3K9acK14acK18acK23acK27acK36me3. Such detail provided by our proteomics platform will be essential for determining how histone modifications occur and act in combination to propagate the histone code during transcriptional events and could greatly enable sequencing of the histone component of human epigenomes.

Hybrid and single feedstock energy processes for liquid transportation fuels: A critical review

Abstract This review provides a detailed account of the key contributions within the energy communities with specific emphasis on thermochemically based hybrid energy systems for liquid transportation fuels. Specifically, the advances in the indirect liquefaction of coal to liquid (CTL), natural gas to liquid (GTL), biomass to liquid (BTL), coal and natural gas to liquid (CGTL), coal and biomass to liquid (CBTL), natural gas and biomass to liquid (BGTL), and coal, biomass, and natural gas to liquid (CBGTL) are presented. This review is the first work that provides a comprehensive description of the contributions for the single-feedstock energy systems and the hybrid feedstock energy systems, for single stand-alone processes and energy supply chain networks. The focus is on contributions in (a) conceptual design, (b) process simulation, (c) economic analysis, (d) heat integration, (e) power integration, (f) water integration, (g) process synthesis, (h) life cycle analysis, (i) sensitivity analysis, (j) uncertainty issues, and (k) supply chain. A classification of the contributions based on the products, as well as different research groups is also provided.

Optimal energy supply network determination and life cycle analysis for hybrid coal, biomass, and natural gas to liquid (CBGTL) plants using carbon-based hydrogen production

A mixed-integer linear optimization formulation is developed to analyze the United States energy supply chain network for the hybrid coal, biomass, and natural gas to liquids (CBGTL) facilities. Each state is discretized into octants and each octant centroid serves as a potential location of one facility. The model selects the optimal locations of CBGTL facilities, the feedstock combination, and size of each facility that gives the minimum overall production cost. Two case studies are presented to investigate the effects of various technologies and hydrogen prices. The CBGTL network is capable to supply transportation fuel demands for the country at a cost between

Optimization framework for the simultaneous process synthesis, heat and power integration of a thermochemical hybrid biomass, coal, and natural gas facility

15.68 and

Biomass to liquid transportation fuels (BTL) systems: process synthesis and global optimization framework

22.06/GJ LHV (

Process synthesis of hybrid coal, biomass, and natural gas to liquids via Fischer–Tropsch synthesis, ZSM-5 catalytic conversion, methanol synthesis, methanol-to-gasoline, and methanol-to-olefins/distillate technologies

76.55-

A Mixed Integer Linear Optimization Framework for the Identification and Quantification of Targeted Post-translational Modifications of Highly Modified Proteins Using Multiplexed Electron Transfer Dissociation Tandem Mass Spectrometry

112.91/bbl crude oil) of produced liquid fuels for both case studies. Life cycle analysis on each facility in the supply chain network shows that the United States fuel demands can be fulfilled with an excess of 50% emissions reduction compared to petroleum based processes

Simultaneous process synthesis, heat, power, and water integration of thermochemical hybrid biomass, coal, and natural gas facilities

Abstract A thermochemical based process superstructure and its mixed-integer nonlinear optimization (MINLP) model are introduced to convert biomass (switchgrass), coal (Illinois #6), and natural gas to liquid (CBGTL) transportation fuels. The MINLP model includes simultaneous heat and power integration utilizing heat engines to recover electricity from the process waste heat. Four case studies are presented to investigate the effect of CO 2 sequestration (CCS) and greenhouse gas (GHG) reduction targets on the process topology along with detailed parametric analysis on the role of biomass and electricity prices. Topological similarities for the case studies include selection of solid/vapor-fueled gasifiers and iron-catalyzed Fischer-Tropsch units that facilitate the reverse water–gas-shift reaction. The break-even oil price was found to be

Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples

57.16/bbl for CCS with a 50% GHG reduction,