Unrestrictive protein modification localization and quality control for open search of mass spectra

2018 ◽  
Author(s):  
Zhiwu An ◽  
Fuzhou Gong ◽  
Yan Fu

We have developed PTMiner, a first software tool for automated, confident filtering, localization and annotation of protein post-translational modifications identified by open (mass-tolerant) search of large tandem mass spectrometry datasets. The performance of the software was validated on carefully designed simulation data. <br>

2018 ◽  
Author(s):  
Zhiwu An ◽  
Fuzhou Gong ◽  
Yan Fu

We have developed PTMiner, a first software tool for automated, confident filtering, localization and annotation of protein post-translational modifications identified by open (mass-tolerant) search of large tandem mass spectrometry datasets. The performance of the software was validated on carefully designed simulation data. <br>


1990 ◽  
Vol 38 (12) ◽  
pp. 3389-3394 ◽  
Author(s):  
Michiaki YONEDA ◽  
Kazuo TSUJIMOTO ◽  
Mamoru OHASHI ◽  
Masami SHIRATSUCHI ◽  
Yasushi OHKAWA ◽  
...  

Author(s):  
Aslam Burhan ◽  
Bhavin Vyas

<p><strong>Objective: </strong>To develop and validate simple, sensitive and selective ultra-performance liquid chromatography and tandem mass spectrometry (UPLC-MS/MS) method for quantification of rifampicin (RIF) in rat plasma and its application to pharmacokinetics study.</p><p><strong>Methods: </strong>Precipitation method was used for the extraction of plasma samples, an aliquot of 25 µl plasma samples was extracted using acetonitrile precipitation technique. Chromatographic separation was performed usingWaters Acquity<sup>TM</sup>UPLC columns, BEH C18 (50 mm× 2.1 mm, 1.7 µm) by a gradient mixture of acetonitrile and water (both containing 0.1 % formic acid) as a mobile phase at the flow rate of 0.7 ml/min.The analyte was protonated in the positive ESI (electrospray ionization interface) and detected in MRM (multiple reactions monitoring) modes using the transition m/z 308.60-455.30.</p><p><strong>Results: </strong>The method had a short chromatography run time of 1.8 min with improved sensitivity over existing methods. Calibration curves been linear over the wide range of 1.97-5047.00 ng/ml. The between and within-batch precision and accuracy of the method was determined by using 4 quality control samples; the highest %CV observed was10.11. The mean recovery values are 74.26, 82.77 and 101.73 at low, medium and high-quality control levels; respectively.</p><p><strong>Conclusion: </strong>It was concluded that the developed and validated UPLC-MS/MS method was sensitive,specific, precise, linear, and rapid. Therefore, the method can be used for quantification of RIFin rat plasma with various advantages over the reported methods. RIF is widely recommended by US-FDAguidance for industry on drug interaction studies and the developed method can be used to explore drug interaction studies in drug discovery and development.</p>


2021 ◽  
Vol 8 ◽  
Author(s):  
Yanyun Wang ◽  
Yun Sun ◽  
Tao Jiang

Background: Tandem mass spectrometry becomes a common and important test in newborn screening, but potential contamination of the equipment has largely been ignored.Methods: The source of contamination through Biosan quality control samples was examined prospectively, and further confirmed by retrospective analysis of patient samples.Results: We found that the source of contamination came from a syringe in the Biosan quality control samples. Furthermore, we found that a large number of indicators in the patient sample were interfered by syringe contamination in our center, and also in two other newborn screening centers, but the affected indicators were different in different screening centers.Conclusion: Syringe contamination will affect the detection of patient samples by tandem mass spectrometry and should be monitored carefully and immediately.


Molecules ◽  
2019 ◽  
Vol 24 (12) ◽  
pp. 2226 ◽  
Author(s):  
Alexander O. Chizhov ◽  
Yury E. Tsvetkov ◽  
Nikolay E. Nifantiev

Modern mass spectrometry, including electrospray and MALDI, is applied for analysis and structure elucidation of carbohydrates. Cyclic oligosaccharides isolated from different sources (bacteria and plants) have been known for decades and some of them (cyclodextrins and their derivatives) are widely used in drug design, as food additives, in the construction of nanomaterials, etc. The peculiarities of the first- and second-order mass spectra of cyclic oligosaccharides (natural, synthetic and their derivatives and modifications: cyclodextrins, cycloglucans, cyclofructans, cyclooligoglucosamines, etc.) are discussed in this minireview.


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