H J Issaq

..Among the 210 proteins identified, 73% and 67% were not found in previous studies of the low-molecular-weight or whole-serum proteome, respectively...

..41-fold increase as determined by Western blotting. These results demonstrate that quantitative proteomics is capable of providing a quantitative view of thousands of proteins in mammalian cells within a defined set of experiments...

..The results presented here provide the broadest proteome coverage for a mammalian cell to date and show that MS-based proteomics has the potential to provide high coverage of the proteins expressed within a cell...

..The results presented here represent the broadest proteome coverage in mouse serum and provide a foundation from which quantitative comparisons can be made in this important animal model...

..Antibody-based analysis of a panel of human melanoma cell lines confirmed that CD13 and SDF-1 were consistently upregulated during hypoxia. This study provides the basis for the discovery of novel hypoxia-induced membrane proteins...

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..Also, a discussion of novel approaches to protein concentration, separation, detection, and quantification is given...

..In this minireview we discuss the application of SELDI-TOF MS to protein biomarker discovery and profiling...

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..A brief discussion of electrophoretic procedures used for protein fractionation and biomarker discovery is also included...

..We evaluated high performance liquid chromatography coupled online with a mass spectrometer metabolomic approach to differentiate urine samples from healthy individuals and patients with bladder cancer...

..The application of each technique is discussed and its advantages and limitations are discussed with selective illustrative examples...

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..This manuscript provides a review of two- and three-dimensional peptide separation strategies combined with MS for the analysis of complex peptide mixtures...

..The total experimental time for the HPLC and capillary electrophoretic analyses ist less than 1 h, which ist much faster than using 2-D slab-gel electrophoresis or single-capillary capillary electrophoresis...

..The advantages and limitations of three sheathless designs are discussed and commented upon, these include single-capillary, two-capillary and three-piece designs...

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..The Sigma DNA replaceable gel gave reproducible results when used as received or diluted at 60%. In our hands hydroxyethyl cellulose gave more reproducible results than polyacrylamide gel...

..Also, the optimum HPLC temperature might be different depending on the fragment sizes to be resolved...

..A discussion of sample extraction and clean-up and the advantages of using CE is also presented...

..A section dealing with recent reviews related to natural products is also included...

..This set-up is practical, simple, robust and allows the separation of complex mixtures. Preliminary results show the utility of this system for the analysis of protein digest...

..Amino acids at a concentration as low as 10 ng/mL could be labeled with fluorescamine. Solid-state UV-LIF detection of the tryptic digest of cytochrome c after fluorescamine derivatization was demonstrated...

..These results indicate that methanol alone or in combination with PPS yielded significantly higher membrane protein identification/enrichment than the PPS alone...

..The resulting peptide maps were compared with corresponding theoretical simulation...

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..The separation of aflatoxin isomers and chlorophenol congeners is presented. In the separation of chlorophenols the more hydrophobic trichlorophenols eluted first and the least hydrophobic, phenol, eluted last...

..This high-speed separation, with minimum postrun data processing, is highly desirable for the high-throughput screening of PCR products using a single-capillary CE system...

..The principle of separation is the same in electrokinetic chromatography with or without electroosmotic flow; however, there are many significant differences that will be highlighted...

..A total of 91 (24%) proteins were classified as integral alpha-helical membrane proteins, of which 51 (56%) were predicted to have multiple transmembrane domains...

..The resulting maps were compared and contrasted with their experimental counterparts. The potential of this approach and its limitations are discussed...

..This requirement is not seen in a deleted Gag protein lacking residues 16-99 within the matrix domain...

..The methodology adopted in this work provides the means for future quantitative measurements in comparative animal models of disease and in human disease cohorts...

..This result confirms previous, targeted studies suggesting that DRMMs isolated using Triton X-100 and Brij-96 differ in their protein content...

..This analysis resulted in the identification of 383 unique proteins in the WCX-2 serum retentate. Among the proteins identified, 50 (13%) are documented clinical biomarkers with 36 of these (72%) identified from multiple peptides...

..Interestingly, the DNA excision repair pathway is enhanced, while integrin and its ligands are downregulated in the cells with long telomeres. These results may provide valuable information related to telomere functions...

..The entire procedure--beginning with isolated membrane fraction and finishing with MS data acquisition--takes 4-5 d...

..The quantitation of the nanoparticles was linear from 0-500 microg/mL with detection limits ranging from 0.5 to 6 microg/mL...

..The study also indicates that evaluation of confidence levels for phosphopeptide identification via the reversed sequence database searching strategy might underestimate the false positive rate...

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..While acquisition of the 2D data require more time, the data obtained resulted in a more meaningful and comprehensive metabolic profile, aided in metabolite identifications, and minimized ambiguities in peak assignments...

..These peptides resulted in identification of 2563 proteins of which 876 (34%) are classified as membrane proteins...

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..The results show that the separation strategy is effective for high-throughput characterization of proteins from complex proteomic mixtures...

..Unlike first-dimensional ion-exchange LC fractionation, where there is a large degree of overlap, the CZE-MS results show less than 15% overlap between neighboring RPLC fractions...

..Testing of this novel CE-MS system showed its ability to characterize proteomic samples such as protein digests, in-gel-digested proteins, and hydrophobic peptides as well as to quantitate ICAT-labeled peptides...

..Injection of 25 fmol of [Glu1]-fibrinopeptide B using the new device produced a CE-ESI-MS electropherogram with a signal-to-noise ratio of over 100 for this peptide...

..Strategies for global, targeted, and quantitative phosphoproteomics are discussed, and some recent interesting applications are also evaluated...

..Preliminary results show that the MEKC-LIF with direct sample injection is a feasible method for assessing indole profiles in diluted urine and serum...

..The large number of proteins identified demonstrates the efficacy of this method for the removal of large abundant proteins and the enrichment of the LMW serum proteome...

..The results show that the separation strategy is effective for high throughput characterization of proteins from complex proteomic mixtures...

..This review will discuss recently published applications of pSFC, with a specific focus on its advantages and limitations for the analysis of pharmaceuticals with varying chemical properties...

..This review will discuss the basics of SELDI protein chip technology and highlight its recent applications in disease biomarker discovery with emphasis on cancer diagnosis...

..The new ICAT reagents were then applied to the analysis of a cortical neuron proteome sample to identify proteins regulated by the antitumor drug, camptothecin...

..Using this bioinformatic approach, we were able to discriminate spectral patterns associated with IC-affected, BC-affected, and unaffected patients with a success rate of approximately 84%...

..In addition, a critical assessment of the overall technology is presented with an emphasis on the steps required to enable proteomic pattern analysis to become a viable clinical tool for diagnosing early-stage cancers...

..The quantitative profiling of Ib-induced DRMP from Vero cells revealed several proteins with altered expression levels suggesting their possible role in Ib binding/uptake...

..Furthermore, 121 proteins from cholesterol-rich plasma membrane domains (caveolar and lipid rafts) were identified...

..This review discusses some of the recent progress made in the development of techniques not only to identify, but also to quantitatively determine sites of phosphorylation...

..e., m/z 400-2000). The results show that GPF(m/z) represents an effective technique for increasing protein identifications in global proteomic investigations especially when sample quantity is limited...

..2% [(2)H(2)]-dA enrichment to 5 pmol at 0.1% [(2)H(2)]-dA enrichment)...

..This investigation represents the first systematic proteomic analysis of MVs and provides insights into both the function and origin of these important mineralization-regulating vesicles...

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..Although micellar EKC gave baseline separation of a standard mixture of 10 EM, the LOQs using UV detection were not suitable for the assay of the low level estrogens in biological samples...

..Thus, an increase in the survival of CD4 T cells appears to be the critical mechanism leading to sustained increases in the CD4 cell counts of HIV-infected patients receiving intermittent IL-2 therapy...

..These data suggest that the repetitive sites are direct targets of Lsh action and that Lsh plays an important role as 'epigenetic guardian' of the genome to protect against deregulation of parasitic retroviral elements...

..Accuracy and precision variation for intra and inter-day validation were below the acceptable limit (15%) for pharmacokinetic studies...

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..In this way, high-resolution analysis of even the minor components in the complicated mixture was possible...

..5 (S/N = 3), and 5 pg, respectively. Compared with RP-HPLC MS analysis of the same mixture in terms of speed of analysis and sensitivity, pSFC MS is much faster, 10 versus 70 min, with comparable LOD and LOQ...

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