PhosAF: An integrated deep learning architecture for predicting protein phosphorylation sites with AlphaFold2 predicted structures
Anal Biochem. 2024 Mar 19;690:115510. doi: 10.1016/j.ab.2024.115510. Online ahead of print.ABSTRACTPhosphorylation is indispensable in comprehending biological processes, while biological experimental methods for identifying phosphorylation sites are tedious and arduous. With the rapid growth of biotechnology, deep learning methods have made significant progress in site prediction tasks. Nevertheless, most existing predictors only consider protein sequence information, that limits the capture of protein spatial information. Building upon the latest advancement in protein structure prediction by AlphaFold2, a novel integrat...
Source: Analytical Biochemistry - March 21, 2024 Category: Biochemistry Authors: Ziyuan Yu Jialin Yu Hongmei Wang Shuai Zhang Long Zhao Shaoping Shi Source Type: research
Comparison of two acquisition modes in mass spectrometry for quantification of 12 antibiotics, including beta-lactams, linezolid, fluoroquinolones and clindamycin: Multiple reactions monitoring (MRM) and fullMS/dd-MS < sup > 2 < /sup >
Anal Biochem. 2024 Mar 19;690:115507. doi: 10.1016/j.ab.2024.115507. Online ahead of print.ABSTRACTThe quantification of antibiotics, using mass spectrometry, for monitoring therapeutic drugs is a key benefit in infection management. After an easy work-up of plasma samples, analysis were performed using both two widely used acquisition modes: MRM for the triple quadrupole spectrometer and fullMS/ddMS2 for the HRMS to quantify twelve antibiotics. Comparison between the two acquisition modes were performed. Validation parameters and sample values were used as comparison criteria. The results indicated a good correlation betw...
Source: Analytical Biochemistry - March 21, 2024 Category: Biochemistry Authors: Catherine Feliu Celine Konecki Damien Vautier Jessica Rogier Claire Gozalo Yoann Cazaubon Zoubir Djerada Source Type: research
PhosAF: An integrated deep learning architecture for predicting protein phosphorylation sites with AlphaFold2 predicted structures
Anal Biochem. 2024 Mar 19:115510. doi: 10.1016/j.ab.2024.115510. Online ahead of print.ABSTRACTPhosphorylation is indispensable in comprehending biological processes, while biological experimental methods for identifying phosphorylation sites are tedious and arduous. With the rapid growth of biotechnology, deep learning methods have made significant progress in site prediction tasks. Nevertheless, most existing predictors only consider protein sequence information, that limits the capture of protein spatial information. Building upon the latest advancement in protein structure prediction by AlphaFold2, a novel integrated d...
Source: Analytical Biochemistry - March 21, 2024 Category: Biochemistry Authors: Ziyuan Yu Jialin Yu Hongmei Wang Shuai Zhang Long Zhao Shaoping Shi Source Type: research
Comparison of two acquisition modes in mass spectrometry for quantification of 12 antibiotics, including beta-lactams, linezolid, fluoroquinolones and clindamycin: Multiple reactions monitoring (MRM) and fullMS/dd-MS < sup > 2 < /sup >
Anal Biochem. 2024 Mar 19:115507. doi: 10.1016/j.ab.2024.115507. Online ahead of print.ABSTRACTThe quantification of antibiotics, using mass spectrometry, for monitoring therapeutic drugs is a key benefit in infection management for many hospitals. After an easy work-up of plasma samples, analysis were performed using both We aimed to evaluate the differences and agreements between the two widely used acquisition modes: MRM for the triple quadrupole spectrometer and fullMS/ddMS2 for the HRMS to quantify twelve antibiotics. Comparison between the two acquisition modes were performed. Validation parameters and sample values ...
Source: Analytical Biochemistry - March 21, 2024 Category: Biochemistry Authors: Catherine Feliu Celine Konecki Damien Vautier Jessica Rogier Claire Gozalo Yoann Cazaubon Zoubir Djerada Source Type: research
PhosAF: An integrated deep learning architecture for predicting protein phosphorylation sites with AlphaFold2 predicted structures
Anal Biochem. 2024 Mar 19:115510. doi: 10.1016/j.ab.2024.115510. Online ahead of print.ABSTRACTPhosphorylation is indispensable in comprehending biological processes, while biological experimental methods for identifying phosphorylation sites are tedious and arduous. With the rapid growth of biotechnology, deep learning methods have made significant progress in site prediction tasks. Nevertheless, most existing predictors only consider protein sequence information, that limits the capture of protein spatial information. Building upon the latest advancement in protein structure prediction by AlphaFold2, a novel integrated d...
Source: Analytical Biochemistry - March 21, 2024 Category: Biochemistry Authors: Ziyuan Yu Jialin Yu Hongmei Wang Shuai Zhang Long Zhao Shaoping Shi Source Type: research
Periodic magnetic modulation enhanced electrochemical analysis for highly sensitive determination of genomic DNA methylation
Anal Biochem. 2024 Mar 18:115509. doi: 10.1016/j.ab.2024.115509. Online ahead of print.ABSTRACTDNA methylation aberrations have a strong correlation with cancer in early detection, diagnosis, and prognosis, which make them possible candidate biomarkers. Electrochemical biosensors offer rapid protocols for detecting DNA methylation status with minimal pretreatment of samples. However, the inevitable presence of background current in the time domain, including electrochemical noise and variations, limits the detection performance of these biosensors, especially for low concentration analytes. Here, we propose an ultrasensiti...
Source: Analytical Biochemistry - March 20, 2024 Category: Biochemistry Authors: Yitao Liang Yu Jiang Lu Fang Zhen Dai Shanshan Zhang Yue Zhou Yu Cai Dong Wang Zhaoyang Wang Xuesong Ye Bo Liang Source Type: research
Periodic magnetic modulation enhanced electrochemical analysis for highly sensitive determination of genomic DNA methylation
Anal Biochem. 2024 Mar 18:115509. doi: 10.1016/j.ab.2024.115509. Online ahead of print.ABSTRACTDNA methylation aberrations have a strong correlation with cancer in early detection, diagnosis, and prognosis, which make them possible candidate biomarkers. Electrochemical biosensors offer rapid protocols for detecting DNA methylation status with minimal pretreatment of samples. However, the inevitable presence of background current in the time domain, including electrochemical noise and variations, limits the detection performance of these biosensors, especially for low concentration analytes. Here, we propose an ultrasensiti...
Source: Analytical Biochemistry - March 20, 2024 Category: Biochemistry Authors: Yitao Liang Yu Jiang Lu Fang Zhen Dai Shanshan Zhang Yue Zhou Yu Cai Dong Wang Zhaoyang Wang Xuesong Ye Bo Liang Source Type: research
Systematically amino acid analysis: Advancements in extinction coefficient determination for therapeutic proteins
Anal Biochem. 2024 Mar 15:115508. doi: 10.1016/j.ab.2024.115508. Online ahead of print.ABSTRACTBiologicals developers often face challenges in accurately determining the extinction coefficient (EC) measurement. We have successfully improved the precision and robustness of the widely recognized amino acid analysis method for EC determination, through a stepwise optimization process. Extensive analyses based on 114 observations, covering eight proteins over three years were performed, with a maximum relative standard deviation of 1.5% among multiple analysts, and a maximum deviation of 2.8% from the theoretical EC across the...
Source: Analytical Biochemistry - March 17, 2024 Category: Biochemistry Authors: Ya Xu Zhenzhen Shao Lei Zhang Yanjing Cao Zhuoyu Liu Zhongli Zhang Source Type: research
Systematically amino acid analysis: Advancements in extinction coefficient determination for therapeutic proteins
Anal Biochem. 2024 Mar 15:115508. doi: 10.1016/j.ab.2024.115508. Online ahead of print.ABSTRACTBiologicals developers often face challenges in accurately determining the extinction coefficient (EC) measurement. We have successfully improved the precision and robustness of the widely recognized amino acid analysis method for EC determination, through a stepwise optimization process. Extensive analyses based on 114 observations, covering eight proteins over three years were performed, with a maximum relative standard deviation of 1.5% among multiple analysts, and a maximum deviation of 2.8% from the theoretical EC across the...
Source: Analytical Biochemistry - March 17, 2024 Category: Biochemistry Authors: Ya Xu Zhenzhen Shao Lei Zhang Yanjing Cao Zhuoyu Liu Zhongli Zhang Source Type: research
Systematically amino acid analysis: Advancements in extinction coefficient determination for therapeutic proteins
Anal Biochem. 2024 Mar 15:115508. doi: 10.1016/j.ab.2024.115508. Online ahead of print.ABSTRACTBiologicals developers often face challenges in accurately determining the extinction coefficient (EC) measurement. We have successfully improved the precision and robustness of the widely recognized amino acid analysis method for EC determination, through a stepwise optimization process. Extensive analyses based on 114 observations, covering eight proteins over three years were performed, with a maximum relative standard deviation of 1.5% among multiple analysts, and a maximum deviation of 2.8% from the theoretical EC across the...
Source: Analytical Biochemistry - March 17, 2024 Category: Biochemistry Authors: Ya Xu Zhenzhen Shao Lei Zhang Yanjing Cao Zhuoyu Liu Zhongli Zhang Source Type: research
Extraction of naturally occurring peptides versus the tryptic digestion of proteins from fetal versus adult bovine serum for LC-ESI-MS/MS
Anal Biochem. 2024 Mar 8:115497. doi: 10.1016/j.ab.2024.115497. Online ahead of print.ABSTRACTThe naturally occurring peptides and digested proteins of fetal versus adult bovine serum were compared by LC-ESI-MS/MS after correction against noise from blank injections and random MS/MS spectra as statistical controls. Serum peptides were extracted by differential precipitation with mixtures of acetonitrile and water. Serum proteins were separated by partition chromatography over quaternary amine resin followed by tryptic digestion. The rigorous X!TANDEM goodness of fit algorithm that has a low error rate as demonstrated by lo...
Source: Analytical Biochemistry - March 10, 2024 Category: Biochemistry Authors: Zhuo Zhen Chen Jaimie Dufresne Peter Bowden Ming Miao John G Marshall Source Type: research
Extraction of naturally occurring peptides versus the tryptic digestion of proteins from fetal versus adult bovine serum for LC-ESI-MS/MS
Anal Biochem. 2024 Mar 8:115497. doi: 10.1016/j.ab.2024.115497. Online ahead of print.ABSTRACTThe naturally occurring peptides and digested proteins of fetal versus adult bovine serum were compared by LC-ESI-MS/MS after correction against noise from blank injections and random MS/MS spectra as statistical controls. Serum peptides were extracted by differential precipitation with mixtures of acetonitrile and water. Serum proteins were separated by partition chromatography over quaternary amine resin followed by tryptic digestion. The rigorous X!TANDEM goodness of fit algorithm that has a low error rate as demonstrated by lo...
Source: Analytical Biochemistry - March 10, 2024 Category: Biochemistry Authors: Zhuo Zhen Chen Jaimie Dufresne Peter Bowden Ming Miao John G Marshall Source Type: research
Extraction of naturally occurring peptides versus the tryptic digestion of proteins from fetal versus adult bovine serum for LC-ESI-MS/MS
Anal Biochem. 2024 Mar 8:115497. doi: 10.1016/j.ab.2024.115497. Online ahead of print.ABSTRACTThe naturally occurring peptides and digested proteins of fetal versus adult bovine serum were compared by LC-ESI-MS/MS after correction against noise from blank injections and random MS/MS spectra as statistical controls. Serum peptides were extracted by differential precipitation with mixtures of acetonitrile and water. Serum proteins were separated by partition chromatography over quaternary amine resin followed by tryptic digestion. The rigorous X!TANDEM goodness of fit algorithm that has a low error rate as demonstrated by lo...
Source: Analytical Biochemistry - March 10, 2024 Category: Biochemistry Authors: Zhuo Zhen Chen Jaimie Dufresne Peter Bowden Ming Miao John G Marshall Source Type: research
Extraction of naturally occurring peptides versus the tryptic digestion of proteins from fetal versus adult bovine serum for LC-ESI-MS/MS
Anal Biochem. 2024 Mar 8:115497. doi: 10.1016/j.ab.2024.115497. Online ahead of print.ABSTRACTThe naturally occurring peptides and digested proteins of fetal versus adult bovine serum were compared by LC-ESI-MS/MS after correction against noise from blank injections and random MS/MS spectra as statistical controls. Serum peptides were extracted by differential precipitation with mixtures of acetonitrile and water. Serum proteins were separated by partition chromatography over quaternary amine resin followed by tryptic digestion. The rigorous X!TANDEM goodness of fit algorithm that has a low error rate as demonstrated by lo...
Source: Analytical Biochemistry - March 10, 2024 Category: Biochemistry Authors: Zhuo Zhen Chen Jaimie Dufresne Peter Bowden Ming Miao John G Marshall Source Type: research
Extraction of naturally occurring peptides versus the tryptic digestion of proteins from fetal versus adult bovine serum for LC-ESI-MS/MS
Anal Biochem. 2024 Mar 8:115497. doi: 10.1016/j.ab.2024.115497. Online ahead of print.ABSTRACTThe naturally occurring peptides and digested proteins of fetal versus adult bovine serum were compared by LC-ESI-MS/MS after correction against noise from blank injections and random MS/MS spectra as statistical controls. Serum peptides were extracted by differential precipitation with mixtures of acetonitrile and water. Serum proteins were separated by partition chromatography over quaternary amine resin followed by tryptic digestion. The rigorous X!TANDEM goodness of fit algorithm that has a low error rate as demonstrated by lo...
Source: Analytical Biochemistry - March 10, 2024 Category: Biochemistry Authors: Zhuo Zhen Chen Jaimie Dufresne Peter Bowden Ming Miao John G Marshall Source Type: research
