@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 {1480,
	title = {Electrospray ionization source geometry for mass spectrometry: past, present, and future},
	journal = {Trac-Trends in Analytical Chemistry},
	volume = {25},
	number = {3},
	year = {2006},
	note = {ISI Document Delivery No.: 026CJTimes Cited: 34Cited Reference Count: 130},
	month = {Mar},
	pages = {243-256},
	type = {Review},
	abstract = {The geometry of an electrospray ion source plays important roles in the processes of analyte desolvation, ionization, transportation, and detection in a mass spectrometer. We provide a brief account of the scientific principles involved in developing an electrospray ion source, and in the various geometries used to improve the sensitivity of mass spectrometry. We also present some popular configurations currently available and outline future trends in this research area. (C) 2005 Elsevier Ltd. All rights reserved.},
	keywords = {ANALYSIS SYSTEMS, atmospheric pressure ionization, ATMOSPHERIC-PRESSURE, CAPILLARY-ZONE-ELECTROPHORESIS, CHARGED DROPLETS, commercial ion source design, electrospray ionization, ion source, ion source geometry, mass, MICRO-ELECTROSPRAY, MICROFLUIDIC DEVICES, NANOSCALE LIQUID-CHROMATOGRAPHY, PRESSURE ION LENS, PROTEIN IDENTIFICATION, SOLUTION FLOW-RATES, SPECTROMETRY},
	isbn = {0165-9936},
	url = {<Go to ISI>://000236314000013},
	author = {Manisali, I. and Chen, D. D. Y. and Schneider, B. B.}
}
@article {1238,
	title = {Statistical evaluation of electrospray tandem mass spectra for optimized peptide fragmentation},
	journal = {Journal of the American Society for Mass Spectrometry},
	volume = {16},
	number = {4},
	year = {2005},
	note = {ISI Document Delivery No.: 911RDTimes Cited: 6Cited Reference Count: 33},
	month = {Apr},
	pages = {505-514},
	type = {Article},
	abstract = {Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has become the method of choice for the analysis of complex peptide mixtures. It combines the separation power of nanoflow LC with highly specific sequence analysis, allowing automated peptide sequencing with high resolution and throughput. For peptide fragmentation, the current experimental setup uses predefined parameters based on the mass-to-charge ratio of the individual precursor. Suitable parameters are typically established by empirical evaluation of fragment spectra of individual peptides used as standards. As a result, nonoptimal fragment spectra are obtained if peptides show fragmentation behavior different from these standards, which often result in the loss of sequence-specific fragment ion information. Here we describe a statistical approach for the systematic evaluation of the quality of individual peptide fragment spectra based on the calculation of their arithmetic mean and standard deviation. The method utilizes the dependence of these parameters on the difference in electric potential across the collision cell to determine the value that results in maximum information content. We show that the method is applicable to fragment spectra generated from a variety of multiply-charged tryptic peptides, over a wide concentration range, and on different types of mass analyzers. We also show how this novel approach can be used to define optimized collision energy settings over a wide mass-to-charge range. (J Am Soc Mass Spectrom 2005,16,505-514) (c) 2005 American Society for Mass Spectrometry},
	keywords = {ALGORITHM, ASSISTED-LASER-DESORPTION/IONIZATION, COLLISION-INDUCED DISSOCIATION, DATABASE SEARCH, MIXTURES, PROTEIN IDENTIFICATION, PROTEOMICS, PROTONATED PEPTIDES, SPECTROMETRY},
	isbn = {1044-0305},
	url = {<Go to ISI>://000228021400010},
	author = {Rogalski, J. C. and Lin, M. S. and Sniatynski, M. J. and Taylor, R. J. and Youhnovski, N. and Przybylski, M. and Kast, J.}
}
@article {5190,
	title = {Ion fragmentation in an electrospray ionization mass spectrometer interface with different gases},
	journal = {Rapid Communications in Mass Spectrometry},
	volume = {15},
	number = {4},
	year = {2001},
	note = {ISI Document Delivery No.: 405PTTimes Cited: 12Cited Reference Count: 43},
	pages = {249-257},
	type = {Article},
	abstract = {Nitrogen, argon, and krypton are used as curtain gases in an electrospray ionization mass spectrometer in an attempt to study the effect of these gases on the extent of ion fragmentation between the orifice and the skimmer of the interface region. A previously published collision model predicts that the degree of ion fragmentation increases with increasing mass of the curtain gas. However, the fragmentation yields are found to be the opposite to that expected. It is believed that the reversed trend with argon and krypton is caused by condensation of the gases within the free jet expansion between the orifice and the skimmer. A condensation parameter can be used to predict the degree of clustering of gases within a free jet expansion. When the condensation parameter is minimized, the predicted trend of fragmentation with mass is observed. Copyright (C) 2001 John Wiley \& Sons, Ltd.},
	keywords = {CONDENSATION, FREE-JET EXPANSIONS, INDUCED DISSOCIATION, LIQUID-HELIUM CLUSTERS, MYOGLOBIN, PERFORMANCE, PROTEIN IDENTIFICATION, SPECTROSCOPY, TECHNOLOGY, TEMPERATURE},
	isbn = {0951-4198},
	url = {<Go to ISI>://000167168800002},
	author = {Schneider, B. S. and Douglas, D. J. and Chan, D. D. Y.}
}
