@article {2648,
	title = {Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring},
	journal = {Journal of Proteomics},
	volume = {72},
	number = {5},
	year = {2009},
	note = {ISI Document Delivery No.: 478RATimes Cited: 5Cited Reference Count: 30Walsh, Geraldine M. Lin, Shujun Evans, Daniel M. Khosrovi-Eghbal, Arash Beavis, Ronald C. Kast, Juergen},
	month = {Jul},
	pages = {838-852},
	type = {Article},
	abstract = {Multiple reaction monitoring (MRM), commonly employed for the mass spectrometric detection of small molecules, is rapidly gaining ground in proteomics. Its high sensitivity and specificity makes this targeted approach particularly useful when sample throughput or proteome coverage limits global studies. Existing tools to design MRM assays rely exclusively on theoretical predictions, or combine them with previous observations on the same type of sample. The additional mass spectrometric experimentation this requires can pose significant demands on time and material. To overcome these challenges, a new MRM worksheet was introduced into The Global Proteome Machine database (GPMDB) that provided all of the information needed to design MRM transitions based solely on archived observations made by other researchers in previous experiments. This required replacing the precursor ion intensity by the number of peptide observations, which proved to be an adequate substitute if peptides did not occur in multiple forms. While the absence of collision energy information proved largely inconsequential, successful prediction of unique transitions depended on the type of fragment ion involved. The design of MRM assays for iTRAQ-labeled tryptic peptides obtained from human platelet proteins demonstrated the usefulness of the MRM worksheet also for quantitative applications. This workflow, which relies exclusively on experimental observations stored in data repositories, therefore represents an attractive alternative for the prediction of MRM transitions prior to experimental validation and optimization. (C) 2008 Elsevier B.V. All rights reserved.},
	keywords = {ABSOLUTE, Data repository, HIGH-SENSITIVITY, LIBRARIES, Multiple reaction monitoring, PEPTIDES, PHOSPHORYLATION, PLASMA-PROTEINS, PLATELETS, PREDICTION, PROTEIN IDENTIFICATION, PROTEOMICS, QUANTIFICATION, SHOTGUN PROTEOMICS, Tandem mass spectrometry, TANDEM MASS-SPECTROMETRY, Targeted},
	isbn = {1874-3919},
	url = {<Go to ISI>://000268604400013},
	author = {Walsh, G. M. and Lin, S. and Evans, D. M. and Khosrovi-Eghbal, A. and Beavis, R. C. and Kast, J.}
}
@article {2072,
	title = {Phage display and crystallographic analysis reveals potential substrate/binding site interactions in the protein secretion chaperone CsaA from Agrobacterium tumefaciens},
	journal = {Journal of Molecular Biology},
	volume = {379},
	number = {3},
	year = {2008},
	note = {ISI Document Delivery No.: 311FQTimes Cited: 0Cited Reference Count: 52Feldman, Anat R. Shapova, Yuliya A. Wu, Sampson S. T. Oliver, David C. Heller, Markus McIntosh, Lawrence P. Scott, Jamie K. Paetzel, Mark},
	month = {Jun},
	pages = {457-470},
	type = {Article},
	abstract = {The protein CsaA has been proposed to function as a protein secretion chaperone in bacteria that lack the Sec-dependent protein-targeting chaperone SecB. CsaA is a homodimer with two putative substrate-binding pockets, one in each monomer. To test the hypothesis that these cavities are indeed substrate-binding sites able to interact with other polypeptide chains, we selected a peptide that bound to CsaA from a random peptide library displayed on phage. Presented here is the structure of CsaA from Agrobacterium tumefaciens (AtCsaA) solved in the presence and absence of the selected peptide. To promote co-crystallization, the sequence for this peptide was genetically fused to the amino-terminus of AtCsaA. The resulting 1.65 angstrom resolution crystal structure reveals that the tethered peptide from one AtCsaA molecule binds to the proposed substrate-binding pocket of a symmetry-related molecule possibly mimicking the interaction between a pre-protein substrate and CsaA. The structure shows that the peptide lies in an extended conformation with alanine, proline and glutamine side chains pointing into the binding pocket. The peptide interacts with the atoms of the AtCsaA-binding pocket via seven direct hydrogen bonds. The side chain of a conserved pocket residue, Arg76, has an "up" conformation when the CsaA-binding site is empty and a "down" conformation when the CsaA-binding site is occupied, suggesting that this residue may function to stabilize the peptide in the binding cavity. The presented aggregation assays, phage-display analysis and structural analysis are consistent with AtCsaA being a general chaperone. The properties of the proposed CsaA-binding pocket/peptide interactions are compared to those from other structurally characterized molecular chaperones. (c) 2008 Elsevier Ltd. All rights reserved.},
	keywords = {BACILLUS-SUBTILIS CSAA, BACTERIAL SIGNAL PEPTIDASE, BINDING PROTEIN, CHANNEL, CRYSTAL-STRUCTURE, CsaA, DISPLAY, LIBRARIES, molecular chaperone, phage, PROTEIN SECRETION, protein targeting, SECA, SEQUENCE, STRUCTURAL SUPERPOSITION, TRANSLOCATION},
	isbn = {0022-2836},
	url = {<Go to ISI>://000256586500006},
	author = {Feldman, A. R. and Shapova, Y. A. and Wu, S. S. T. and Oliver, D. C. and Heller, M. and McIntosh, L. P. and Scott, J. K. and Paetzel, M.}
}
@article {497,
	title = {Multiple sprayer system for high-throughput electrospray ionization mass spectrometry},
	journal = {Rapid Communications in Mass Spectrometry},
	volume = {16},
	number = {20},
	year = {2002},
	note = {ISI Document Delivery No.: 604ADTimes Cited: 13Cited Reference Count: 32},
	pages = {1982-1990},
	type = {Article},
	abstract = {<p>A multiple sprayer electrospray ion source for high-throughput analysis is described. The ion source is comprised of multiple electrospray capillaries, each with an ion lens located near the tip. The electric potentials applied to the ion lenses are used to control the sprayers. The use of ion lenses eliminates the need for mechanical blocking devices to selectively enable or disable the sprayers, and results in a less expensive and more reliable set-up. Sprayers can be enabled or disabled within approximately 50-250 ms when the lens potentials are controlled manually. For simultaneous operation of multiple electrospray capillaries, it is advantageous to orient the capillaries so that the spray from each passes directly in front of the entrance aperture of the mass spectrometer. Copyright (C) 2002 John Wiley Sons, Ltd.</p>},
	keywords = {ARRAYS, capillary electrophoresis, INTERFACE, LIBRARIES, LIQUID CHROMATOGRAPHY/MASS SPECTROMETRY, SEPARATE SAMPLE},
	isbn = {0951-4198},
	doi = {10.1002/rcm.806},
	url = {https://onlinelibrary.wiley.com/doi/full/10.1002/rcm.806},
	author = {Schneider, B. B. and Douglas, D. J. and Chen, D. D. Y.}
}
