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Journal articles on the topic 'Mass spectrometry proteomics in Ruby'

Author: Grafiati

Published: 4 June 2021

Last updated: 10 February 2022

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1

Prince, J. T., and E. M. Marcotte. "mspire: mass spectrometry proteomics in Ruby." Bioinformatics 24, no. 23 (2008): 2796–97. http://dx.doi.org/10.1093/bioinformatics/btn513.

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2

Akar, Nejat, Duygu Ozel Demiralp, Ibrahim C. Haznedaroglu, and Hakan Goker. "Functional Proteomics of Ankaferd Blood Stopper." Blood 112, no. 11 (2008): 4103. http://dx.doi.org/10.1182/blood.v112.11.4103.4103.

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Abstract Ankaferd Blood Stopper (ABS) comprises a standardized mixture of the plants Thymus vulgaris, Glycyrrhiza glabra, Vitis vinifera, Alpinia officinarum and Urtica dioica. The basic mechanism of action for ABS is the formation of an encapsulated protein network that provides focal points for vital erythrocyte aggregation. ABS–induced protein network formation with blood cells particularly erythrocytes covers the primary and secondary haemostatic system without disturbing individual coagulation factors (Figure 1). The aim of this study is to perform functional proteomic analyses of ABS, wh

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3

Lannert, Heinrich, Thomas Able, Thomas Franz, et al. "G-CSF Stimulates Expression of Non-Phosphorylated Stathmin (Oncoprotein, Op18) in Hematopoietic Stem Cells." Blood 110, no. 11 (2007): 2215. http://dx.doi.org/10.1182/blood.v110.11.2215.2215.

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Abstract Stathmin/Op18 is a cytosolic phosphoprotein which regulates the dynamics of microtubules. This regulation is important in mitosis during cell division and in the migration of cells in modification of the cytoskeleton. In this study we investigated native hematopoietic CD34+ stem cells (HSCs) from BM in comparison to mobilized peripheral blood stem cells (mPBSCs) from G-CSF stimulated healthy donors. All the cell fractions were highly enriched (&gt;99%). In comparative proteome analysis mPBSCs showed high levels of Stathmin compared to native HSCs from BM. We monitored Stathmin by

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4

Wada, Kazuya, Atsushi Ogiwara, Keiko Nagasaka, Naoki Tanaka, and Yasuhiko Komatsu. "i-RUBY: A novel software for quantitative analysis of highly accurate shotgun-proteomics liquid chromatography/tandem mass spectrometry data obtained without stable-isotope labeling of proteins." Rapid Communications in Mass Spectrometry 25, no. 7 (2011): 960–68. http://dx.doi.org/10.1002/rcm.4943.

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5

Thongboonkerd, Visith, Jon B. Klein, William M. Pierce, Anthony W. Jevans, and John M. Arthur. "Sodium loading changes urinary protein excretion: a proteomic analysis." American Journal of Physiology-Renal Physiology 284, no. 6 (2003): F1155—F1163. http://dx.doi.org/10.1152/ajprenal.00140.2002.

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Plasma sodium concentration is maintained even when sodium intake is altered. Sodium homeostasis may involve changes in renal tubular protein expression that are reflected in the urine. We used proteomic analysis to investigate changes in urinary protein excretion in response to acute sodium loading. Rats were given deionized water followed by hypertonic (2.7%) saline for 28 h each. Urinary protein expression was determined during the final 4 h of each treatment. Acute sodium loading increased urinary sodium excretion (4.53 ± 1.74 vs. 1.70 ± 0.27 mmol/day, P = 0.029). Urinary proteins were sep

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6

Nock, Christina M., Malcolm S. Ball, Ian R. White, J. Mark Skehel, Louisa Bill, and Peter Karuso. "Mass spectrometric compatibility of Deep Purple and SYPRO Ruby total protein stains for high-throughput proteomics using large-format two-dimensional gel electrophoresis." Rapid Communications in Mass Spectrometry 22, no. 6 (2008): 881–86. http://dx.doi.org/10.1002/rcm.3483.

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7

Lannert, Heinrich, Thomas Franz, Volker Eckstein, et al. "Quantitative and Qualitative Protein Expression Mapping of Highly Enriched G-CSF Mobilized CD34+ Stem Cells from Peripheral Blood." Blood 104, no. 11 (2004): 4130. http://dx.doi.org/10.1182/blood.v104.11.4130.4130.

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Abstract Background: Proteome analysis is a direct measurement of proteins in terms of their presence and relative abundance in a defined system. The overall aim of a proteomic study is characterization of the complex network of cell regulation. Different states of a cell can be compared and specific qualitative and quantitative protein changes can be identified. We focused our first proteom-investigations on G-CSF mobilized CD34+ stem cells from peripheral blood (PB). Methods: Mononuclear cells from healthy donors were isolated by a standard Ficoll-Hypaque gradient separation method after leu

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8

Antohe, F. "Mass Spectrometry Based Proteomics." Acta Endocrinologica (Bucharest) 11, no. 2 (2015): 139–42. http://dx.doi.org/10.4183/aeb.2015.139.

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9

PATTERSON, SCOTT D. "Mass spectrometry and proteomics." Physiological Genomics 2, no. 2 (2000): 59–65. http://dx.doi.org/10.1152/physiolgenomics.2000.2.2.59.

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10

McCormack, Ashley L. "Mass spectrometry in proteomics." Methods 35, no. 3 (2005): 209–10. http://dx.doi.org/10.1016/j.ymeth.2004.08.012.

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11

Gygi, Steven P., and Ruedi Aebersold. "Mass spectrometry and proteomics." Current Opinion in Chemical Biology 4, no. 5 (2000): 489–94. http://dx.doi.org/10.1016/s1367-5931(00)00121-6.

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12

Aebersold, Ruedi, and Matthias Mann. "Mass spectrometry-based proteomics." Nature 422, no. 6928 (2003): 198–207. http://dx.doi.org/10.1038/nature01511.

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13

Aebersold, Ruedi, and David R. Goodlett. "Mass Spectrometry in Proteomics." Chemical Reviews 101, no. 2 (2001): 269–96. http://dx.doi.org/10.1021/cr990076h.

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14

Han, Xuemei, Aaron Aslanian, and John R. Yates. "Mass spectrometry for proteomics." Current Opinion in Chemical Biology 12, no. 5 (2008): 483–90. http://dx.doi.org/10.1016/j.cbpa.2008.07.024.

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15

Hood, Brian L., Timothy D. Veenstra, and Thomas P. Conrads. "Mass spectrometry-based proteomics." International Congress Series 1266 (April 2004): 375–80. http://dx.doi.org/10.1016/j.ics.2004.02.087.

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16

Takao, Toshifumi. "Mass Spectrometry and Proteomics Research." TRENDS IN THE SCIENCES 8, no. 2 (2003): 60–61. http://dx.doi.org/10.5363/tits.8.2_60.

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17

Baudin, Bruno. "Mass spectrometry and clinical proteomics." Annales de biologie clinique 73, no. 1 (2015): 39–48. http://dx.doi.org/10.1684/abc.2014.1019.

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18

Heck, Albert JR, and Jeroen Krijgsveld. "Mass spectrometry-based quantitative proteomics." Expert Review of Proteomics 1, no. 3 (2004): 317–26. http://dx.doi.org/10.1586/14789450.1.3.317.

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19

Bantscheff, Marcus, and Bernhard Kuster. "Quantitative mass spectrometry in proteomics." Analytical and Bioanalytical Chemistry 404, no. 4 (2012): 937–38. http://dx.doi.org/10.1007/s00216-012-6261-7.

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20

Sechi, Salvatore, and Yoshiya Oda. "Quantitative proteomics using mass spectrometry." Current Opinion in Chemical Biology 7, no. 1 (2003): 70–77. http://dx.doi.org/10.1016/s1367-5931(02)00010-8.

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21

Pusch, Wolfgang, Mark T. Flocco, Sau-Mei Leung, Herbert Thiele, and Markus Kostrzewa. "Mass spectrometry-based clinical proteomics." Pharmacogenomics 4, no. 4 (2003): 463–76. http://dx.doi.org/10.1517/phgs.4.4.463.22753.

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22

Käll, Lukas, and Olga Vitek. "Computational Mass Spectrometry–Based Proteomics." PLoS Computational Biology 7, no. 12 (2011): e1002277. http://dx.doi.org/10.1371/journal.pcbi.1002277.

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23

Doerr, Allison. "Mass spectrometry–based targeted proteomics." Nature Methods 10, no. 1 (2013): 23. http://dx.doi.org/10.1038/nmeth.2286.

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24

Serpa, Jason J., Carol E. Parker, Evgeniy V. Petrotchenko, Jun Han, Jingxi Pan, and Christoph H. Borchers. "Mass Spectrometry-Based Structural Proteomics." European Journal of Mass Spectrometry 18, no. 2 (2012): 251–67. http://dx.doi.org/10.1255/ejms.1178.

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25

Bakhtiar, Ray, John J. Thomas, and Gary Siuzdak. "Mass Spectrometry in Viral Proteomics." Accounts of Chemical Research 33, no. 3 (2000): 179–87. http://dx.doi.org/10.1021/ar9801200.

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26

Koch, Inge, Peter Hoffmann, and J. S. Marron. "Proteomics profiles from mass spectrometry." Electronic Journal of Statistics 8, no. 2 (2014): 1703–13. http://dx.doi.org/10.1214/14-ejs900.

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27

Canas, B. "Mass spectrometry technologies for proteomics." Briefings in Functional Genomics and Proteomics 4, no. 4 (2006): 295–320. http://dx.doi.org/10.1093/bfgp/eli002.

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28

Nakamura, Tatsuji, and Yoshiya Oda. "Mass spectrometry-based quantitative proteomics." Biotechnology and Genetic Engineering Reviews 24, no. 1 (2007): 147–64. http://dx.doi.org/10.1080/02648725.2007.10648097.

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29

Gershon, Diane. "Mass spectrometry: gaining mass appeal in proteomics." Nature Methods 2, no. 6 (2005): 465–72. http://dx.doi.org/10.1038/nmeth0605-465.

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30

Nakayama, Hiroshi. "Proteomics using liquid chromatography-Mass spectrometry." SEIBUTSU BUTSURI KAGAKU 44, no. 2 (2000): 91–95. http://dx.doi.org/10.2198/sbk.44.91.

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31

Gygi, Steven P., and Ruedi Aebersold. "Using mass spectrometry for quantitative proteomics." Trends in Biotechnology 18 (July 2000): 31–36. http://dx.doi.org/10.1016/s0167-7799(00)00008-1.

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32

Valle de Sousa, Marcelo. "Is Proteomics Possible Without Mass Spectrometry?" Brazilian Journal of Analytical Chemistry 7, no. 29 (2020): 11–12. http://dx.doi.org/10.30744/brjac.2179-3425.point-of-view-mvsousa.

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33

Moghieb, Ahmed, Manasi Mangaonkar, and Kevin K. W. Wang. "Mass spectrometry based translational neuroinjury proteomics." Translational Proteomics 1, no. 1 (2013): 65–73. http://dx.doi.org/10.1016/j.trprot.2013.07.001.

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34

Wepf, Alexander, Timo Glatter, Alexander Schmidt, Ruedi Aebersold, and Matthias Gstaiger. "Quantitative interaction proteomics using mass spectrometry." Nature Methods 6, no. 3 (2009): 203–5. http://dx.doi.org/10.1038/nmeth.1302.

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35

Thiele, Herbert. "Mass Spectrometry and Bioinformatics in Proteomics." CHANCE 16, no. 4 (2003): 29–51. http://dx.doi.org/10.1080/09332480.2003.10554872.

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36

Ong, Shao-En, and Matthias Mann. "Mass spectrometry–based proteomics turns quantitative." Nature Chemical Biology 1, no. 5 (2005): 252–62. http://dx.doi.org/10.1038/nchembio736.

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37

Rolland, Delphine C. M., Megan S. Lim, and Kojo S. J. Elenitoba-Johnson. "Mass spectrometry and proteomics in hematology." Seminars in Hematology 56, no. 1 (2019): 52–57. http://dx.doi.org/10.1053/j.seminhematol.2018.05.009.

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38

Reinders, Joerg, Urs Lewandrowski, Jan Moebius, Yvonne Wagner, and Albert Sickmann. "Challenges in mass spectrometry-based proteomics." PROTEOMICS 4, no. 12 (2004): 3686–703. http://dx.doi.org/10.1002/pmic.200400869.

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39

Aebersold, Ruedi, and David R. Goodlett. "ChemInform Abstract: Mass Spectrometry in Proteomics." ChemInform 32, no. 18 (2001): no. http://dx.doi.org/10.1002/chin.200118270.

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40

Xu, Guang, Jacek Stupak, Li Yang, Luokai Hu, Bo Guo, and Jianjun Li. "Deconvolution in mass spectrometry based proteomics." Rapid Communications in Mass Spectrometry 32, no. 10 (2018): 763–74. http://dx.doi.org/10.1002/rcm.8103.

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41

Webb-Robertson, B. "Computational methods for mass spectrometry proteomics." Journal of the American Society for Mass Spectrometry 19, no. 11 (2008): R3—R4. http://dx.doi.org/10.1016/j.jasms.2008.07.009.

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42

Mann, Matthias. "Origins of mass spectrometry-based proteomics." Nature Reviews Molecular Cell Biology 17, no. 11 (2016): 678. http://dx.doi.org/10.1038/nrm.2016.135.

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43

Doerr, Allison. "Focus on mass spectrometry in proteomics." Nature Methods 4, no. 10 (2007): 781. http://dx.doi.org/10.1038/nmeth1007-781.

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44

Schulze, Waltraud X., and Björn Usadel. "Quantitation in Mass-Spectrometry-Based Proteomics." Annual Review of Plant Biology 61, no. 1 (2010): 491–516. http://dx.doi.org/10.1146/annurev-arplant-042809-112132.

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45

Sokolowska, Izabela, Armand G. Ngounou Wetie, Alisa G. Woods, and Costel C. Darie. "Applications of Mass Spectrometry in Proteomics." Australian Journal of Chemistry 66, no. 7 (2013): 721. http://dx.doi.org/10.1071/ch13137.

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Characterisation of proteins and whole proteomes can provide a foundation to our understanding of physiological and pathological states and biological diseases or disorders. Constant development of more reliable and accurate mass spectrometry (MS) instruments and techniques has allowed for better identification and quantification of the thousands of proteins involved in basic physiological processes. Therefore, MS-based proteomics has been widely applied to the analysis of biological samples and has greatly contributed to our understanding of protein functions, interactions, and dynamics, adva

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46

Guerrera, Ida Chiara, and Oliver Kleiner. "Application of Mass Spectrometry in Proteomics." Bioscience Reports 25, no. 1-2 (2005): 71–93. http://dx.doi.org/10.1007/s10540-005-2849-x.

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Mass spectrometry has arguably become the core technology in proteomics. The application of mass spectrometry based techniques for the qualitative and quantitative analysis of global proteome samples derived from complex mixtures has had a big impact in the understanding of cellular function. Here, we give a brief introduction to principles of mass spectrometry and instrumentation currently used in proteomics experiments. In addition, recent developments in the application of mass spectrometry in proteomics are summarised. Strategies allowing high-throughput identification of proteins from hig

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47

Sanz-Medel, Alfredo, María Montes-Bayón, María del Rosario Fernández de la Campa, Jorge Ruiz Encinar, and Jörg Bettmer. "Elemental mass spectrometry for quantitative proteomics." Analytical and Bioanalytical Chemistry 390, no. 1 (2007): 3–16. http://dx.doi.org/10.1007/s00216-007-1615-2.

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48

Zhu, Wenhong, Jeffrey W. Smith, and Chun-Ming Huang. "Mass Spectrometry-Based Label-Free Quantitative Proteomics." Journal of Biomedicine and Biotechnology 2010 (2010): 1–6. http://dx.doi.org/10.1155/2010/840518.

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In order to study the differential protein expression in complex biological samples, strategies for rapid, highly reproducible and accurate quantification are necessary. Isotope labeling and fluorescent labeling techniques have been widely used in quantitative proteomics research. However, researchers are increasingly turning to label-free shotgun proteomics techniques for faster, cleaner, and simpler results. Mass spectrometry-based label-free quantitative proteomics falls into two general categories. In the first are the measurements of changes in chromatographic ion intensity such as peptid

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49

Brancia, Francesco. "Mass Spectrometry Based Strategies in Quantitative Proteomics." Current Analytical Chemistry 2, no. 1 (2006): 1–7. http://dx.doi.org/10.2174/157341106775197367.

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50

ISHIHAMA, Yasushi. "Analytical Platforms for Mass Spectrometry-Based Proteomics." CHROMATOGRAPHY 40, no. 3 (2019): 89–97. http://dx.doi.org/10.15583/jpchrom.2019.023.

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