@article {doi:10.1002/elps.201900452,
	title = {Bottom-up proteomics of envelope proteins extracted from spinach chloroplast via high-organic-content capillary electrophoresis-mass spectrometry},
	journal = {ELECTROPHORESIS},
	volume = {41},
	number = {n/a},
	year = {2020},
	month = {01/2020},
	pages = {370-378},
	type = {Research},
	chapter = {370},
	abstract = {<p>A high-organic-content capillary electrophoresis-tandem mass spectrometry (HOCE-MS/MS) method was developed for the proteomic analysis of envelope proteins extracted from spinach leaves. Separation was performed in a 1-meter long hydroxypropyl cellulose (HPC)-coated capillary, using 8\% (V/V) formic acid (FA) in 70\% (V/V) methanol and 22\% water as the background electrolyte (BGE). A flow-through microvial interface was used to couple the CE system with an Orbitrap Fusion Lumos mass spectrometer, and field-amplified sample stacking was used to improve the concentration sensitivity. Using this optimized method, 3579 peptides and 1141 proteins were identified using the Proteome Discoverer software with a 1\% false discovery rate at the protein level. Relative to conventional aqueous CE, HOCE-MS did a better job of discovering hydrophobic peptides and provided more peptide and protein identifications. Relative to NanoLC-MS, it achieved comparable peptide and protein identification performance and detected peptides not identified by LC-MS: of the full set of peptides identified using the two techniques, 19\% were identified only using HOCE-MS. It also outperformed NanoLC-MS with respect to the detection of low molecular weight peptides. This article is protected by copyright. All rights reserved</p>},
	keywords = {high-organic-content capillary electrophoresis, hydrophobic peptides, proteomics of envelope proteins, spinach chloroplast, Tandem mass spectrometry},
	doi = {10.1002/elps.201900452},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/elps.201900452},
	author = {Cheng, Jianhui and Morin, Gregg B. and Chen, David D. Y.}
}
@article {MA201829,
	title = {Characterization of plant polysaccharides from Dendrobium officinale by multiple chromatographic and mass spectrometric techniques},
	journal = {Journal of Chromatography A},
	volume = {1547},
	year = {2018},
	pages = {29 - 36},
	keywords = {Liquid chromatography, POLYSACCHARIDES, Tandem mass spectrometry},
	issn = {0021-9673},
	doi = {https://doi.org/10.1016/j.chroma.2018.03.006},
	url = {http://www.sciencedirect.com/science/article/pii/S0021967318302784},
	author = {Huiying Ma and Keke Zhang and Qing Jiang and Diya Dai and Hongli Li and Wentao Bi and David Da Yong Chen}
}
@article {2663,
	title = {A Carboxy-Terminal Affinity Tag for the Purification and Mass Spectrometric Characterization of Integral Membrane Proteins},
	journal = {Journal of Proteome Research},
	volume = {8},
	number = {5},
	year = {2009},
	note = {ISI Document Delivery No.: 441BWTimes Cited: 3Cited Reference Count: 22Wong, Julie P. Reboul, Emmanuelle Molday, Robert S. Kast, Juergen},
	month = {May},
	pages = {2388-2396},
	type = {Article},
	abstract = {G-protein-coupled receptors (GPCRs) and other structurally and functionally related membrane proteins represent particularly attractive targets for drug discovery. Integral membrane proteins are often difficult to purify from native contexts, and lack of sufficient quantities hampers subsequent structural and functional proteomic studies. We describe here an optimized enrichment strategy involving a membrane protein-compatible 1D4 affinity tag that is derived from the carboxy-terminal nine amino residues of bovine rhodopsin, and its corresponding tag-specific, high-affinity monoclonal antibody. When two GPCRs as well as two related ATP binding cassette (ABC) transporters are expressed in their functional forms in human cell lines, we have shown that a single detergent and wash condition can be employed for the purification of all said membrane proteins. Subsequent in-gel digestion with trypsin and mass spectrometric peptide analysis resulted in high sequence coverage for the ABC transporters ABCA1-1D4 and ABCA4-1D4. In contrast, digestion by various enzymatic combinations was necessary to obtain the best sequence coverage for affinity-enriched GPCRs CXCR4-1D4 and CCR5-1D4 as compared against other entries in an annotated spectrum library. Furthermore, specific enzyme combinations were necessary to produce suitable peptides for deducing N-glycosylation sites on CXCR4. Our results demonstrate that the 1D4-tag enrichment strategy is a versatile tool for the characterization of integral membrane proteins that can be employed for functional proteomic studies.},
	keywords = {1D4 affinity tag, 2-DIMENSIONAL, annotated spectrum libraries, ATP binding cassette transporters, BINDING, ELECTROPHORESIS, EXPRESSION, G-protein-coupled, membrane protein enrichment, N-LINKED GLYCOSYLATION, PROTEOMICS, proteotypic peptides, RECEPTOR, RECEPTORS, RHODOPSIN, ROD OUTER SEGMENTS, SITES, SYNTHETIC PEPTIDES, Tandem mass spectrometry},
	isbn = {1535-3893},
	url = {<Go to ISI>://000265745300025},
	author = {Wong, J. P. and Reboul, E. and Molday, R. S. and Kast, J.}
}
@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 {4077,
	title = {Analysis of polyaromatic quinones in a complex environmental matrix using gas chromatography ion trap tandem mass spectrometry},
	journal = {Talanta},
	volume = {44},
	number = {6},
	year = {1997},
	note = {ISI Document Delivery No.: XC195Times Cited: 13Cited Reference Count: 21},
	month = {Jun},
	pages = {985-1001},
	type = {Article},
	abstract = {GC/MS and GC/MS/MS in a quadrupole ion trap were used to analyze for anthraquinone, alkyl anthraquinones, benz[a]anthracene-7,12-dione and 9-fluoranone in a sediment obtained from an aluminum smelter settling pond contaminated with polycyclic aromatic hydrocarbons. By standard GC/MS analysis many of these target compounds were either undetectable or their confirmation uncertain because of matrix interferences. Detection and identification were greatly improved by using GC/MS/MS. GC/MS/MS analyses were performed by selecting the molecular ion (M) of a target compound and fragmenting it via collision induced dissociation (CID) to yield product ions corresponding to loss of CO for unsubstituted compounds or CO plus CH3 for alkylated compounds. The CID conditions were optimized using anthraquinone and 2-methylanthraquinone standards by varying the CID excitation energy and RF storage levels to yield optimum amounts of fragment ions. CID experiments were performed using both resonant and non-resonant wave forms. Although both excitation techniques gave comparable results for the removal of matrix interferences, non-resonant excitation provided more characteristic spectra for the alkylated anthraquinones. Monitoring of secondary fragmentation products, such as M-2CO, provided greater discrimination from matrix interferences than the use of primary fragmentation products, such as M-CO. (C) 1997 Elsevier Science B.V.},
	keywords = {CHROMATOGRAPHY, collision induced dissociation, environmental analysis, GAS, ION TRAP, polyaromatic quinones, polycyclic aromatic hydrocarbons, Tandem mass spectrometry},
	isbn = {0039-9140},
	url = {<Go to ISI>://A1997XC19500006},
	author = {Mosi, A. A. and Reimer, K. J. and Eigendorf, G. K.}
}
