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Showing 1 to 8 of 8 entries
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Mass spectrometry for translational proteomics: progress and clinical implications.

Genome medicine

Baker ES, Liu T, Petyuk VA, Burnum-Johnson KE, Ibrahim YM, Anderson GA, Smith RD.
PMID: 22943415
Genome Med. 2012 Aug 31;4(8):63. doi: 10.1186/gm364. eCollection 2012.

The utility of mass spectrometry (MS)-based proteomic analyses and their clinical applications have been increasingly recognized over the past decade due to their high sensitivity, specificity and throughput. MS-based proteomic measurements have been used in a wide range of...

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Baker ES, Liu T, Petyuk VA, et al. Mass spectrometry for translational proteomics: progress and clinical implications. Genome Med. 2012;4(8):63doi: 10.1186/gm364.
Baker, E. S., Liu, T., Petyuk, V. A., Burnum-Johnson, K. E., Ibrahim, Y. M., Anderson, G. A., & Smith, R. D. (2012). Mass spectrometry for translational proteomics: progress and clinical implications. Genome medicine, 4(8), 63. https://doi.org/10.1186/gm364
Baker, Erin Shammel, et al. "Mass spectrometry for translational proteomics: progress and clinical implications." Genome medicine vol. 4,8 (2012): 63. doi: https://doi.org/10.1186/gm364
Baker ES, Liu T, Petyuk VA, Burnum-Johnson KE, Ibrahim YM, Anderson GA, Smith RD. Mass spectrometry for translational proteomics: progress and clinical implications. Genome Med. 2012 Aug 31;4(8):63. doi: 10.1186/gm364. eCollection 2012. PMID: 22943415; PMCID: PMC3580401.
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Correction: Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability.

Cell reports. Medicine

McDermott JE, Arshad OA, Petyuk VA, Fu Y, Gritsenko MA, Clauss TR, Moore RJ, Schepmoes AA, Zhao R, Monroe ME, Schnaubelt M, Tsai CF, Payne SH, Huang C, Wang LB, Foltz S, Wyczalkowski M, Wu Y, Song E, Brewer MA, Thiagarajan M, Kinsinger CR, Robles AI, Boja ES, Rodriguez H, Chan DW, Zhang B, Zhang Z, Ding L, Smith RD, Liu T, Rodland KD.
PMID: 32954372
Cell Rep Med. 2020 Aug 25;1(5). doi: 10.1016/j.xcrm.2020.100075.

[This corrects the article PMC7289043.].

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McDermott JE, Arshad OA, Petyuk VA, et al. Correction: Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. Cell Rep Med. 2020;1(5)doi: 10.1016/j.xcrm.2020.100075.
McDermott, J. E., Arshad, O. A., Petyuk, V. A., Fu, Y., Gritsenko, M. A., Clauss, T. R., Moore, R. J., Schepmoes, A. A., Zhao, R., Monroe, M. E., Schnaubelt, M., Tsai, C. F., Payne, S. H., Huang, C., Wang, L. B., Foltz, S., Wyczalkowski, M., Wu, Y., Song, E., Brewer, M. A., Thiagarajan, M., Kinsinger, C. R., Robles, A. I., Boja, E. S., Rodriguez, H., Chan, D. W., Zhang, B., Zhang, Z., Ding, L., Smith, R. D., Liu, T., Rodland, K. D. (2020). Correction: Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. Cell reports. Medicine, 1(5), . https://doi.org/10.1016/j.xcrm.2020.100075
McDermott, Jason E, et al. "Correction: Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability." Cell reports. Medicine vol. 1,5 (2020). doi: https://doi.org/10.1016/j.xcrm.2020.100075
McDermott JE, Arshad OA, Petyuk VA, Fu Y, Gritsenko MA, Clauss TR, Moore RJ, Schepmoes AA, Zhao R, Monroe ME, Schnaubelt M, Tsai CF, Payne SH, Huang C, Wang LB, Foltz S, Wyczalkowski M, Wu Y, Song E, Brewer MA, Thiagarajan M, Kinsinger CR, Robles AI, Boja ES, Rodriguez H, Chan DW, Zhang B, Zhang Z, Ding L, Smith RD, Liu T, Rodland KD. Correction: Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. Cell Rep Med. 2020 Aug 25;1(5). doi: 10.1016/j.xcrm.2020.100075. PMID: 32954372; PMCID: PMC7500561.
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Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data.

Expert opinion on medical diagnostics

McDermott JE, Wang J, Mitchell H, Webb-Robertson BJ, Hafen R, Ramey J, Rodland KD.
PMID: 23335946
Expert Opin Med Diagn. 2013 Jan;7(1):37-51. doi: 10.1517/17530059.2012.718329.

INTRODUCTION: The advent of high throughput technologies capable of comprehensive analysis of genes, transcripts, proteins and other significant biological molecules has provided an unprecedented opportunity for the identification of molecular markers of disease processes. However, it has simultaneously complicated...

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McDermott JE, Wang J, Mitchell H, et al. Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data. Expert Opin Med Diagn. 2013;7(1):37-51doi: 10.1517/17530059.2012.718329.
McDermott, J. E., Wang, J., Mitchell, H., Webb-Robertson, B. J., Hafen, R., Ramey, J., & Rodland, K. D. (2013). Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data. Expert opinion on medical diagnostics, 7(1), 37-51. https://doi.org/10.1517/17530059.2012.718329
McDermott, Jason E, et al. "Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data." Expert opinion on medical diagnostics vol. 7,1 (2013): 37-51. doi: https://doi.org/10.1517/17530059.2012.718329
McDermott JE, Wang J, Mitchell H, Webb-Robertson BJ, Hafen R, Ramey J, Rodland KD. Challenges in Biomarker Discovery: Combining Expert Insights with Statistical Analysis of Complex Omics Data. Expert Opin Med Diagn. 2013 Jan;7(1):37-51. doi: 10.1517/17530059.2012.718329. PMID: 23335946; PMCID: PMC3548234.
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Residual tissue repositories as a resource for population-based cancer proteomic studies.

Clinical proteomics

Piehowski PD, Petyuk VA, Sontag RL, Gritsenko MA, Weitz KK, Fillmore TL, Moon J, Makhlouf H, Chuaqui RF, Boja ES, Rodriguez H, Lee JSH, Smith RD, Carrick DM, Liu T, Rodland KD.
PMID: 30087585
Clin Proteomics. 2018 Aug 03;15:26. doi: 10.1186/s12014-018-9202-4. eCollection 2018.

BACKGROUND: Mass spectrometry-based proteomics has become a powerful tool for the identification and quantification of proteins from a wide variety of biological specimens. To date, the majority of studies utilizing tissue samples have been carried out on prospectively collected...

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Piehowski PD, Petyuk VA, Sontag RL, et al. Residual tissue repositories as a resource for population-based cancer proteomic studies. Clin Proteomics. 2018;15:26doi: 10.1186/s12014-018-9202-4.
Piehowski, P. D., Petyuk, V. A., Sontag, R. L., Gritsenko, M. A., Weitz, K. K., Fillmore, T. L., Moon, J., Makhlouf, H., Chuaqui, R. F., Boja, E. S., Rodriguez, H., Lee, J. S. H., Smith, R. D., Carrick, D. M., Liu, T., & Rodland, K. D. (2018). Residual tissue repositories as a resource for population-based cancer proteomic studies. Clinical proteomics, 1526. https://doi.org/10.1186/s12014-018-9202-4
Piehowski, Paul D, et al. "Residual tissue repositories as a resource for population-based cancer proteomic studies." Clinical proteomics vol. 15 (2018): 26. doi: https://doi.org/10.1186/s12014-018-9202-4
Piehowski PD, Petyuk VA, Sontag RL, Gritsenko MA, Weitz KK, Fillmore TL, Moon J, Makhlouf H, Chuaqui RF, Boja ES, Rodriguez H, Lee JSH, Smith RD, Carrick DM, Liu T, Rodland KD. Residual tissue repositories as a resource for population-based cancer proteomic studies. Clin Proteomics. 2018 Aug 03;15:26. doi: 10.1186/s12014-018-9202-4. eCollection 2018. PMID: 30087585; PMCID: PMC6074037.
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Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells.

Communications biology

Shi T, Gaffrey MJ, Fillmore TL, Nicora CD, Yi L, Zhang P, Shukla AK, Wiley HS, Rodland KD, Liu T, Smith RD, Qian WJ.
PMID: 30271983
Commun Biol. 2018 Aug 06;1:103. doi: 10.1038/s42003-018-0107-6. eCollection 2018.

There is an unmet technical challenge for mass spectrometry (MS)-based proteomic analysis of single mammalian cells. Quantitative proteomic analysis of single cells has been previously achieved by antibody-based immunoassays but is limited by the availability of high-quality antibodies. Herein...

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Shi T, Gaffrey MJ, Fillmore TL, et al. Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells. Commun Biol. 2018;1:103doi: 10.1038/s42003-018-0107-6.
Shi, T., Gaffrey, M. J., Fillmore, T. L., Nicora, C. D., Yi, L., Zhang, P., Shukla, A. K., Wiley, H. S., Rodland, K. D., Liu, T., Smith, R. D., & Qian, W. J. (2018). Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells. Communications biology, 1103. https://doi.org/10.1038/s42003-018-0107-6
Shi, Tujin, et al. "Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells." Communications biology vol. 1 (2018): 103. doi: https://doi.org/10.1038/s42003-018-0107-6
Shi T, Gaffrey MJ, Fillmore TL, Nicora CD, Yi L, Zhang P, Shukla AK, Wiley HS, Rodland KD, Liu T, Smith RD, Qian WJ. Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells. Commun Biol. 2018 Aug 06;1:103. doi: 10.1038/s42003-018-0107-6. eCollection 2018. PMID: 30271983; PMCID: PMC6123794.
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Development of a New Ion Mobility (Quadrupole) Time-of-Flight Mass Spectrometer.

International journal of mass spectrometry

Ibrahim YM, Baker ES, Danielson WF, Norheim RV, Prior DC, Anderson GA, Belov ME, Smith RD.
PMID: 26185483
Int J Mass Spectrom. 2015 Feb 01;377:655-662. doi: 10.1016/j.ijms.2014.07.034.

A new ion mobility spectrometer (IMS) platform was developed to improve upon the sensitivity and reproducibility of our previous platforms, and further enhance IMS-MS utility for broad 'pan-omics' measurements. The new platform incorporated an improved electrospray ionization source and...

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Ibrahim YM, Baker ES, Danielson WF, et al. Development of a New Ion Mobility (Quadrupole) Time-of-Flight Mass Spectrometer. Int J Mass Spectrom. 2015;377:655-662doi: 10.1016/j.ijms.2014.07.034.
Ibrahim, Y. M., Baker, E. S., Danielson, W. F., Norheim, R. V., Prior, D. C., Anderson, G. A., Belov, M. E., & Smith, R. D. (2015). Development of a New Ion Mobility (Quadrupole) Time-of-Flight Mass Spectrometer. International journal of mass spectrometry, 377655-662. https://doi.org/10.1016/j.ijms.2014.07.034
Ibrahim, Yehia M, et al. "Development of a New Ion Mobility (Quadrupole) Time-of-Flight Mass Spectrometer." International journal of mass spectrometry vol. 377 (2015): 655-662. doi: https://doi.org/10.1016/j.ijms.2014.07.034
Ibrahim YM, Baker ES, Danielson WF, Norheim RV, Prior DC, Anderson GA, Belov ME, Smith RD. Development of a New Ion Mobility (Quadrupole) Time-of-Flight Mass Spectrometer. Int J Mass Spectrom. 2015 Feb 01;377:655-662. doi: 10.1016/j.ijms.2014.07.034. PMID: 26185483; PMCID: PMC4501404.
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Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry.

International journal of mass spectrometry

Crowell KL, Baker ES, Payne SH, Ibrahim YM, Monroe ME, Slysz GW, LaMarche BL, Petyuk VA, Piehowski PD, Danielson WF, Anderson GA, Smith RD.
PMID: 25089116
Int J Mass Spectrom. 2013 Nov 15;354:312-317. doi: 10.1016/j.ijms.2013.06.028.

Ion mobility spectrometry in conjunction with liquid chromatography separations and mass spectrometry offers a range of new possibilities for analyzing complex biological samples. To fully utilize the information obtained from these three measurement dimensions, informatics tools based on the...

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Crowell KL, Baker ES, Payne SH, et al. Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry. Int J Mass Spectrom. 2013;354:312-317doi: 10.1016/j.ijms.2013.06.028.
Crowell, K. L., Baker, E. S., Payne, S. H., Ibrahim, Y. M., Monroe, M. E., Slysz, G. W., LaMarche, B. L., Petyuk, V. A., Piehowski, P. D., Danielson, W. F., Anderson, G. A., & Smith, R. D. (2013). Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry. International journal of mass spectrometry, 354312-317. https://doi.org/10.1016/j.ijms.2013.06.028
Crowell, Kevin L, et al. "Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry." International journal of mass spectrometry vol. 354 (2013): 312-317. doi: https://doi.org/10.1016/j.ijms.2013.06.028
Crowell KL, Baker ES, Payne SH, Ibrahim YM, Monroe ME, Slysz GW, LaMarche BL, Petyuk VA, Piehowski PD, Danielson WF, Anderson GA, Smith RD. Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry. Int J Mass Spectrom. 2013 Nov 15;354:312-317. doi: 10.1016/j.ijms.2013.06.028. PMID: 25089116; PMCID: PMC4114398.
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Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability.

Cell reports. Medicine

McDermott JE, Arshad OA, Petyuk VA, Fu Y, Gritsenko MA, Clauss TR, Moore RJ, Schepmoes AA, Zhao R, Monroe ME, Schnaubelt M, Tsai CF, Payne SH, Huang C, Wang LB, Foltz S, Wyczalkowski M, Wu Y, Song E, Brewer MA, Thiagarajan M, Kinsinger CR, Robles AI, Boja ES, Rodriguez H, Chan DW, Zhang B, Zhang Z, Ding L, Smith RD, Liu T, Rodland KD.
PMID: 32529193
Cell Rep Med. 2020 Apr 21;1(1). doi: 10.1016/j.xcrm.2020.100004. Epub 2020 Apr 10.

In the absence of a dominant driving mutation other than uniformly present TP53 mutations, deeper understanding of the biology driving ovarian high-grade serous cancer (HGSC) requires analysis at a functional level, including post-translational modifications. Comprehensive proteogenomic and phosphoproteomic characterization...

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McDermott JE, Arshad OA, Petyuk VA, et al. Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. Cell Rep Med. 2020;1(1)doi: 10.1016/j.xcrm.2020.100004.
McDermott, J. E., Arshad, O. A., Petyuk, V. A., Fu, Y., Gritsenko, M. A., Clauss, T. R., Moore, R. J., Schepmoes, A. A., Zhao, R., Monroe, M. E., Schnaubelt, M., Tsai, C. F., Payne, S. H., Huang, C., Wang, L. B., Foltz, S., Wyczalkowski, M., Wu, Y., Song, E., Brewer, M. A., Thiagarajan, M., Kinsinger, C. R., Robles, A. I., Boja, E. S., Rodriguez, H., Chan, D. W., Zhang, B., Zhang, Z., Ding, L., Smith, R. D., Liu, T., Rodland, K. D. (2020). Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. Cell reports. Medicine, 1(1), . https://doi.org/10.1016/j.xcrm.2020.100004
McDermott, Jason E, et al. "Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability." Cell reports. Medicine vol. 1,1 (2020). doi: https://doi.org/10.1016/j.xcrm.2020.100004
McDermott JE, Arshad OA, Petyuk VA, Fu Y, Gritsenko MA, Clauss TR, Moore RJ, Schepmoes AA, Zhao R, Monroe ME, Schnaubelt M, Tsai CF, Payne SH, Huang C, Wang LB, Foltz S, Wyczalkowski M, Wu Y, Song E, Brewer MA, Thiagarajan M, Kinsinger CR, Robles AI, Boja ES, Rodriguez H, Chan DW, Zhang B, Zhang Z, Ding L, Smith RD, Liu T, Rodland KD. Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability. Cell Rep Med. 2020 Apr 21;1(1). doi: 10.1016/j.xcrm.2020.100004. Epub 2020 Apr 10. PMID: 32529193; PMCID: PMC7289043.
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