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Rapid and sensitive profiling and quantification of the human cell line proteome by LC-MS/MS without prefractionation.

Proteomics

Yin X, Liu X, Zhang Y, Yan G, Wang F, Lu H, Shen H, Yang P.
PMID: 25044409
Proteomics. 2014 Sep;14(17):2008-16. doi: 10.1002/pmic.201300510. Epub 2014 Aug 13.

In this paper, we demonstrate a rapid and reproducible 1D LC-MS/MS workflow for fast quantitative proteomic research. We have optimized the LC-MS/MS conditions, including digestion and gradient conditions, sample loading amount, and MS parameter settings. As a result, we...

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Yin X, Liu X, Zhang Y, et al. Rapid and sensitive profiling and quantification of the human cell line proteome by LC-MS/MS without prefractionation. Proteomics. 2014;14(17):2008-16doi: 10.1002/pmic.201300510.
Yin, X., Liu, X., Zhang, Y., Yan, G., Wang, F., Lu, H., Shen, H., & Yang, P. (2014). Rapid and sensitive profiling and quantification of the human cell line proteome by LC-MS/MS without prefractionation. Proteomics, 14(17), 2008-16. https://doi.org/10.1002/pmic.201300510
Yin, Xuefei, et al. "Rapid and sensitive profiling and quantification of the human cell line proteome by LC-MS/MS without prefractionation." Proteomics vol. 14,17 (2014): 2008-16. doi: https://doi.org/10.1002/pmic.201300510
Yin X, Liu X, Zhang Y, Yan G, Wang F, Lu H, Shen H, Yang P. Rapid and sensitive profiling and quantification of the human cell line proteome by LC-MS/MS without prefractionation. Proteomics. 2014 Sep;14(17):2008-16. doi: 10.1002/pmic.201300510. Epub 2014 Aug 13. PMID: 25044409.
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Curatr: a web application for creating, curating and sharing a mass spectral library.

Bioinformatics (Oxford, England)

Palmer A, Phapale P, Fay D, Alexandrov T.
PMID: 29253079
Bioinformatics. 2018 Apr 15;34(8):1436-1438. doi: 10.1093/bioinformatics/btx786.

SUMMARY: We have developed a web application curatr for the rapid generation of high quality mass spectral fragmentation libraries from liquid-chromatography mass spectrometry datasets. Curatr handles datasets from single or multiplexed standards and extracts chromatographic profiles and potential fragmentation...

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Palmer A, Phapale P, Fay D, et al. Curatr: a web application for creating, curating and sharing a mass spectral library. Bioinformatics. 2018;34(8):1436-1438doi: 10.1093/bioinformatics/btx786.
Palmer, A., Phapale, P., Fay, D., & Alexandrov, T. (2018). Curatr: a web application for creating, curating and sharing a mass spectral library. Bioinformatics (Oxford, England), 34(8), 1436-1438. https://doi.org/10.1093/bioinformatics/btx786
Palmer, Andrew, et al. "Curatr: a web application for creating, curating and sharing a mass spectral library." Bioinformatics (Oxford, England) vol. 34,8 (2018): 1436-1438. doi: https://doi.org/10.1093/bioinformatics/btx786
Palmer A, Phapale P, Fay D, Alexandrov T. Curatr: a web application for creating, curating and sharing a mass spectral library. Bioinformatics. 2018 Apr 15;34(8):1436-1438. doi: 10.1093/bioinformatics/btx786. PMID: 29253079.
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pH-Gradient Liquid Chromatography: Fundamentals and Examples.

Journal of AOAC International

Kubik Ł, Wiczling P, Kaliszan R.
PMID: 28703096
J AOAC Int. 2017 Nov 01;100(6):1590-1598. doi: 10.5740/jaoacint.17-0205. Epub 2017 Jul 13.

In this paper, we acquaint the readers with the fundamentals of gradient separation, followed by the latest innovations in this field. We describe the principles of organic modifier- and pH-gradient elution emphasizing the differences and similarities with isocratic separation....

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Kubik Ł, Wiczling P, Kaliszan R. pH-Gradient Liquid Chromatography: Fundamentals and Examples. J AOAC Int. 2017;100(6):1590-1598doi: 10.5740/jaoacint.17-0205.
Kubik, �. �., Wiczling, P., & Kaliszan, R. (2017). pH-Gradient Liquid Chromatography: Fundamentals and Examples. Journal of AOAC International, 100(6), 1590-1598. https://doi.org/10.5740/jaoacint.17-0205
Kubik, Łukasz, et al. "pH-Gradient Liquid Chromatography: Fundamentals and Examples." Journal of AOAC International vol. 100,6 (2017): 1590-1598. doi: https://doi.org/10.5740/jaoacint.17-0205
Kubik Ł, Wiczling P, Kaliszan R. pH-Gradient Liquid Chromatography: Fundamentals and Examples. J AOAC Int. 2017 Nov 01;100(6):1590-1598. doi: 10.5740/jaoacint.17-0205. Epub 2017 Jul 13. PMID: 28703096.
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Post-acquisition data mining techniques for LC-MS/MS-acquired data in drug metabolite identification.

Bioanalysis

Dhurjad PS, Marothu VK, Rathod R.
PMID: 28816067
Bioanalysis. 2017 Aug;9(16):1265-1278. doi: 10.4155/bio-2017-0046. Epub 2017 Aug 17.

Metabolite identification is a crucial part of the drug discovery process. LC-MS/MS-based metabolite identification has gained widespread use, but the data acquired by the LC-MS/MS instrument is complex, and thus the interpretation of data becomes troublesome. Fortunately, advancements in...

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Dhurjad PS, Marothu VK, Rathod R. Post-acquisition data mining techniques for LC-MS/MS-acquired data in drug metabolite identification. Bioanalysis. 2017;9(16):1265-1278doi: 10.4155/bio-2017-0046.
Dhurjad, P. S., Marothu, V. K., & Rathod, R. (2017). Post-acquisition data mining techniques for LC-MS/MS-acquired data in drug metabolite identification. Bioanalysis, 9(16), 1265-1278. https://doi.org/10.4155/bio-2017-0046
Dhurjad, Pooja Sukhdev, et al. "Post-acquisition data mining techniques for LC-MS/MS-acquired data in drug metabolite identification." Bioanalysis vol. 9,16 (2017): 1265-1278. doi: https://doi.org/10.4155/bio-2017-0046
Dhurjad PS, Marothu VK, Rathod R. Post-acquisition data mining techniques for LC-MS/MS-acquired data in drug metabolite identification. Bioanalysis. 2017 Aug;9(16):1265-1278. doi: 10.4155/bio-2017-0046. Epub 2017 Aug 17. PMID: 28816067.
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Is SPE necessary for environmental analysis? A quantitative comparison of matrix effects from large-volume injection and solid-phase extraction based methods.

Environmental science & technology

Backe WJ, Field JA.
PMID: 22626028
Environ Sci Technol. 2012 Jun 19;46(12):6750-8. doi: 10.1021/es300235z. Epub 2012 Jun 06.

Environmental analysis by large-volume injection (LVI) was compared to solid-phase extraction (SPE) based methods using matrix effects as a quantitative indicator of analytical signal quality. LVI was performed by the direct injection of 900 μL of wastewater onto a...

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Backe WJ, Field JA. Is SPE necessary for environmental analysis? A quantitative comparison of matrix effects from large-volume injection and solid-phase extraction based methods. Environ Sci Technol. 2012;46(12):6750-8doi: 10.1021/es300235z.
Backe, W. J., & Field, J. A. (2012). Is SPE necessary for environmental analysis? A quantitative comparison of matrix effects from large-volume injection and solid-phase extraction based methods. Environmental science & technology, 46(12), 6750-8. https://doi.org/10.1021/es300235z
Backe, Will J, and Field, Jennifer A. "Is SPE necessary for environmental analysis? A quantitative comparison of matrix effects from large-volume injection and solid-phase extraction based methods." Environmental science & technology vol. 46,12 (2012): 6750-8. doi: https://doi.org/10.1021/es300235z
Backe WJ, Field JA. Is SPE necessary for environmental analysis? A quantitative comparison of matrix effects from large-volume injection and solid-phase extraction based methods. Environ Sci Technol. 2012 Jun 19;46(12):6750-8. doi: 10.1021/es300235z. Epub 2012 Jun 06. PMID: 22626028.
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Characterization of stationary phases by a linear solvation energy relationship utilizing supercritical fluid chromatography.

Journal of separation science

Mitchell CR, Benz NJ, Zhang S.
PMID: 20730839
J Sep Sci. 2010 Oct;33(19):3060-7. doi: 10.1002/jssc.201000371.

Supercritical fluid chromatography was utilized in combination with the Abraham model of linear solvation energy relationship to characterize 11 different HPLC stationary phases. System constants were determined at one supercritical fluid chromatography condition for each stationary phase. The results...

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Mitchell CR, Benz NJ, Zhang S. Characterization of stationary phases by a linear solvation energy relationship utilizing supercritical fluid chromatography. J Sep Sci. 2010;33(19):3060-7doi: 10.1002/jssc.201000371.
Mitchell, C. R., Benz, N. J., & Zhang, S. (2010). Characterization of stationary phases by a linear solvation energy relationship utilizing supercritical fluid chromatography. Journal of separation science, 33(19), 3060-7. https://doi.org/10.1002/jssc.201000371
Mitchell, Clifford R, et al. "Characterization of stationary phases by a linear solvation energy relationship utilizing supercritical fluid chromatography." Journal of separation science vol. 33,19 (2010): 3060-7. doi: https://doi.org/10.1002/jssc.201000371
Mitchell CR, Benz NJ, Zhang S. Characterization of stationary phases by a linear solvation energy relationship utilizing supercritical fluid chromatography. J Sep Sci. 2010 Oct;33(19):3060-7. doi: 10.1002/jssc.201000371. PMID: 20730839.
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Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification.

Journal of visualized experiments : JoVE

High AA, Tan H, Pagala VR, Niu M, Cho JH, Wang X, Bai B, Peng J.
PMID: 29286450
J Vis Exp. 2017 Nov 15;(129). doi: 10.3791/56474.

Many exceptional advances have been made in mass spectrometry (MS)-based proteomics, with particular technical progress in liquid chromatography (LC) coupled to tandem mass spectrometry (LC-MS/MS) and isobaric labeling multiplexing capacity. Here, we introduce a deep-proteomics profiling protocol that combines...

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High AA, Tan H, Pagala VR, et al. Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification. J Vis Exp. 2017;(129)doi: 10.3791/56474.
High, A. A., Tan, H., Pagala, V. R., Niu, M., Cho, J. H., Wang, X., Bai, B., & Peng, J. (2017). Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification. Journal of visualized experiments : JoVE, (129), . https://doi.org/10.3791/56474
High, Anthony A, et al. "Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification." Journal of visualized experiments : JoVE vol. ,129 (2017). doi: https://doi.org/10.3791/56474
High AA, Tan H, Pagala VR, Niu M, Cho JH, Wang X, Bai B, Peng J. Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification. J Vis Exp. 2017 Nov 15;(129). doi: 10.3791/56474. PMID: 29286450; PMCID: PMC5755397.
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Machine Learning in Mass Spectrometric Analysis of DIA Data.

Proteomics

Xu LL, Young A, Zhou A, Röst HL.
PMID: 32061181
Proteomics. 2020 Nov;20(21):e1900352. doi: 10.1002/pmic.201900352. Epub 2020 Mar 04.

Liquid Chromatography coupled to Tandem Mass Spectrometry (LC-MS/MS) based methods are currently the top choice for high-throughput, quantitative measurements of the proteome. While traditional proteomics LC-MS/MS methods can suffer from issues such as low reproducibility and quantitative accuracy due...

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Xu LL, Young A, Zhou A, et al. Machine Learning in Mass Spectrometric Analysis of DIA Data. Proteomics. 2020;20(21):e1900352doi: 10.1002/pmic.201900352.
Xu, L. L., Young, A., Zhou, A., & Röst, H. L. (2020). Machine Learning in Mass Spectrometric Analysis of DIA Data. Proteomics, 20(21), e1900352. https://doi.org/10.1002/pmic.201900352
Xu, Leon L, et al. "Machine Learning in Mass Spectrometric Analysis of DIA Data." Proteomics vol. 20,21 (2020): e1900352. doi: https://doi.org/10.1002/pmic.201900352
Xu LL, Young A, Zhou A, Röst HL. Machine Learning in Mass Spectrometric Analysis of DIA Data. Proteomics. 2020 Nov;20(21):e1900352. doi: 10.1002/pmic.201900352. Epub 2020 Mar 04. PMID: 32061181.
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Editorial.

Journal of chromatography. B, Analytical technologies in the biomedical and life sciences

Hage DS.
PMID: 31670110
J Chromatogr B Analyt Technol Biomed Life Sci. 2019 Nov 01;1130:121804. doi: 10.1016/j.jchromb.2019.121804. Epub 2019 Oct 04.

No abstract available.

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Hage DS. Editorial. J Chromatogr B Analyt Technol Biomed Life Sci. 2019;1130:121804doi: 10.1016/j.jchromb.2019.121804.
Hage, D. S. (2019). Editorial. Journal of chromatography. B, Analytical technologies in the biomedical and life sciences, 1130121804. https://doi.org/10.1016/j.jchromb.2019.121804
Hage, David S. "Editorial." Journal of chromatography. B, Analytical technologies in the biomedical and life sciences vol. 1130 (2019): 121804. doi: https://doi.org/10.1016/j.jchromb.2019.121804
Hage DS. Editorial. J Chromatogr B Analyt Technol Biomed Life Sci. 2019 Nov 01;1130:121804. doi: 10.1016/j.jchromb.2019.121804. Epub 2019 Oct 04. PMID: 31670110.
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Systematic evaluation of supported liquid extraction in reducing matrix effect and improving extraction efficiency in LC-MS/MS based bioanalysis for 10 model pharmaceutical compounds.

Journal of chromatography. B, Analytical technologies in the biomedical and life sciences

Jiang H, Cao H, Zhang Y, Fast DM.
PMID: 22410088
J Chromatogr B Analyt Technol Biomed Life Sci. 2012 Apr 01;891:71-80. doi: 10.1016/j.jchromb.2012.02.031. Epub 2012 Feb 23.

In past a few years, there has been a large increase in the application of supported liquid extraction (SLE) for LC-MS/MS based bioanalysis due to its distinct practical advantage in reduced time cost, ease of operation and the feasibility...

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Jiang H, Cao H, Zhang Y, et al. Systematic evaluation of supported liquid extraction in reducing matrix effect and improving extraction efficiency in LC-MS/MS based bioanalysis for 10 model pharmaceutical compounds. J Chromatogr B Analyt Technol Biomed Life Sci. 2012;891:71-80doi: 10.1016/j.jchromb.2012.02.031.
Jiang, H., Cao, H., Zhang, Y., & Fast, D. M. (2012). Systematic evaluation of supported liquid extraction in reducing matrix effect and improving extraction efficiency in LC-MS/MS based bioanalysis for 10 model pharmaceutical compounds. Journal of chromatography. B, Analytical technologies in the biomedical and life sciences, 89171-80. https://doi.org/10.1016/j.jchromb.2012.02.031
Jiang, Hongliang, et al. "Systematic evaluation of supported liquid extraction in reducing matrix effect and improving extraction efficiency in LC-MS/MS based bioanalysis for 10 model pharmaceutical compounds." Journal of chromatography. B, Analytical technologies in the biomedical and life sciences vol. 891 (2012): 71-80. doi: https://doi.org/10.1016/j.jchromb.2012.02.031
Jiang H, Cao H, Zhang Y, Fast DM. Systematic evaluation of supported liquid extraction in reducing matrix effect and improving extraction efficiency in LC-MS/MS based bioanalysis for 10 model pharmaceutical compounds. J Chromatogr B Analyt Technol Biomed Life Sci. 2012 Apr 01;891:71-80. doi: 10.1016/j.jchromb.2012.02.031. Epub 2012 Feb 23. PMID: 22410088.
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Method selection for liquid chromatography.

Analytical methods : advancing methods and applications

Analytical Methods Committee Amctb No.
PMID: 34241604
Anal Methods. 2021 Jul 22;13(28):3205-3208. doi: 10.1039/d1ay90086b.

The accurate measurement of trace level substances in complex mixtures requires advanced instrumental techniques that generally use some form of separation prior to analysis, such as chromatography. There is an increasing trend for users that do not specialise in...

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Analytical Methods Committee Amctb No. Method selection for liquid chromatography. Anal Methods. 2021;13(28):3205-3208doi: 10.1039/d1ay90086b.
Analytical Methods Committee Amctb No. (2021). Method selection for liquid chromatography. Analytical methods : advancing methods and applications, 13(28), 3205-3208. https://doi.org/10.1039/d1ay90086b
Analytical Methods Committee Amctb No. "Method selection for liquid chromatography." Analytical methods : advancing methods and applications vol. 13,28 (2021): 3205-3208. doi: https://doi.org/10.1039/d1ay90086b
Analytical Methods Committee Amctb No. Method selection for liquid chromatography. Anal Methods. 2021 Jul 22;13(28):3205-3208. doi: 10.1039/d1ay90086b. PMID: 34241604.
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Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro.

Journal of proteome research

Aballo TJ, Roberts DS, Melby JA, Buck KM, Brown KA, Ge Y.
PMID: 34236868
J Proteome Res. 2021 Aug 06;20(8):4203-4211. doi: 10.1021/acs.jproteome.1c00446. Epub 2021 Jul 08.

Global bottom-up mass spectrometry (MS)-based proteomics is widely used for protein identification and quantification to achieve a comprehensive understanding of the composition, structure, and function of the proteome. However, traditional sample preparation methods are time-consuming, typically including overnight tryptic...

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Aballo TJ, Roberts DS, Melby JA, et al. Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro. J Proteome Res. 2021;20(8):4203-4211doi: 10.1021/acs.jproteome.1c00446.
Aballo, T. J., Roberts, D. S., Melby, J. A., Buck, K. M., Brown, K. A., & Ge, Y. (2021). Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro. Journal of proteome research, 20(8), 4203-4211. https://doi.org/10.1021/acs.jproteome.1c00446
Aballo, Timothy J, et al. "Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro." Journal of proteome research vol. 20,8 (2021): 4203-4211. doi: https://doi.org/10.1021/acs.jproteome.1c00446
Aballo TJ, Roberts DS, Melby JA, Buck KM, Brown KA, Ge Y. Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro. J Proteome Res. 2021 Aug 06;20(8):4203-4211. doi: 10.1021/acs.jproteome.1c00446. Epub 2021 Jul 08. PMID: 34236868; PMCID: PMC8349881.
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Showing 1 to 12 of 144 entries