MMS2plot: An R Package for Visualizing Multiple MS/MS Spectra for Groups of Modified and Non‐Modified Peptides

A large number of post‐translational modifications (PTMs) in proteins are buried in the unassigned mass spectrometric (MS) spectra in shot‐gun proteomics datasets. Because the modified peptide fragments are low in abundance relative to the corresponding non‐modified versions, it is critical to develop tools that allow facile evaluation of assignment of PTMs based on the MS/MS spectra. Such tools will preferably have the ability to allow comparison of fragment ion spectra and retention time between the modified and unmodified peptide pairs or group. Herein, MMS2plot, an R package for visualizing peptide‐spectrum matches (PSMs) for multiple peptides, is described. MMS2plot features a batch mode and generates the output images in vector graphics file format that facilitate evaluation and publication of the PSM assignment. MMS2plot is expected to play an important role in PTM discovery from large‐scale proteomics datasets generated by liquid chromatography‐MS/MS. The MMS2plot package is freely available at https://github.com/lileir/MMS2plot under the GPL‐3 license.     

A green and effective method for the determination of metalaxyl enantiomers in tobacco and soil by supercritical fluid chromatography–tandem mass spectrometry

We reported a new methodology for the stereoselective determination of metalaxyl enantiomers in tobacco and soil. The QuEChERS (quick, easy, cheap, effective, rugged, and safe) method was used for the extraction and clean-up of the tobacco and soil samples. Separation of the metalaxyl enantiomers was performed on an ACQUITY UPC2 Trefoil CEL1 chiral column coupled with supercritical fluid chromatography with tandem mass spectrometry (SFC-MS/MS), and the run time was only 5 minutes. Under the optimized conditions, the recoveries for the enantiomers were between 78.2% and 93.3% with intraday relative standard deviations (RSDs) ranging from 1.1% to 5.4%. The limit of detection (LOD) for the enantiomers in tobacco and soil varied from 0.005 to 0.007 mg/kg, and the limit of quantitation (LOQ) ranged from 0.017 to 0.020 mg/kg. In this method, only a small amount of methanol was consumed to obtain a rapid stereoselective separation. This proposed method showed good accuracy and precision and might be suitable for fast enantioselective determination of metalaxyl in food and environmental samples. The developed method was further validated by application to the analysis of authentic samples.     

糜蛋白酶提高膜蛋白质谱分析序列覆盖率的胶内消化方法

近年来,质谱技术在膜蛋白结构与功能研究中被广泛应用。由于膜蛋白的跨膜结构域含有大量疏水性氨基酸,常常导致液质串联质谱检测的序列覆盖率较低,从而限制了质谱技术在膜蛋白结构与功能研究中的应用。文中利用人的整合膜蛋白维生素K环氧化物还原酶为模型,优化胶内消化条件,建立了一种稳定提高膜蛋白质谱序列覆盖率的糜蛋白酶胶内消化方法。通过探索钙离子浓度、pH值和缓冲体系对序列覆盖率、检测特异肽段的总数和类型以及特异肽段大小的影响,发现在5–10 mmol/L钙离子浓度、pH 8.0–8.5的Tris-HCl缓冲液中,可以兼顾序列覆盖率和肽段的多样性。该方法可以使膜蛋白的质谱覆盖率达到80%以上,将在膜蛋白结构与功能、膜蛋白相互作用位点的鉴定以及膜蛋白与小分子药物结合位点的鉴定等研究中具有广泛的应用价值。