Simple Tool for Rapidly Assessing the Quality of Multiplexed Single Cell Proteomics Data.
Simple Tool for Rapidly Assessing the Quality of Multiplexed Single Cell Proteomics Data.
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DOI：
10.1021/jasms.3c00238
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发表时间：
2023-12-06
影响因子：
3.2
通讯作者：
Orsburn, Benjamin C.
中科院分区：
文献类型：
--
作者：
Jenkins, Conor;Orsburn, Benjamin C.
质谱仪灵敏度和速度的最新进展加上改进的样品制备方法使得单细胞蛋白质组学领域得以蓬勃发展。虽然无标签空间正在大力发展，但通过串联质量标签的复用可显着提高吞吐量。使用这种方法可以分析数百或数千个单细胞，产生大量数据集，其中可能包含由于细胞分选过程中材料损失或消化、标记和裂解不良而产生的不良数据。迄今为止，还没有描述可以在数据处理之前评估数据质量的工具。我们在此提出了一个轻量级的 python 脚本和随附的图形用户界面，可以快速量化文件中每个 MS/MS 谱图中的报告离子峰。通过简单的汇总报告，我们可以识别未能通过设定质量阈值的单细胞样本，从而减少分析时间浪费。此外，该工具诊断离子数据分析缩减 (DIDAR) 将创建缩减的 MGF 文件，其中仅包含具有用户指定数量的单细胞报告离子的谱图。通过减少具有过多零值的光谱数量，我们可以加快样本处理速度，而数据完整性几乎没有损失，因为这些光谱在数据处理工作流程的后期阶段被删除。 DIDAR 和 DIDAR GUI 与所有现代操作系统兼容，可从以下位置获取： 。本研究中描述的所有文件均可在登录号 MSV000088887 中获得。
Recent advances in the sensitivity and speed of mass spectrometers coupled with improved sample preparation methods have enabled the field of single cell proteomics to proliferate. While heavy development is occurring in the label free space, dramatic improvements in throughput are provided by multiplexing with tandem mass tags. Hundreds or thousands of single cells can be analyzed with this method, yielding large data sets which may contain poor data arising from loss of material during cell sorting or poor digestion, labeling, and lysis. To date, no tools have been described that can assess data quality prior to data processing. We present herein a lightweight python script and accompanying graphic user interface that can rapidly quantify reporter ion peaks within each MS/MS spectrum in a file. With simple summary reports, we can identify single cell samples that fail to pass a set quality threshold, thus reducing analysis time waste. In addition, this tool, Diagnostic Ion Data Analysis Reduction (DIDAR), will create reduced MGF files containing only spectra possessing a user-specified number of single cell reporter ions. By reducing the number of spectra that have excessive zero values, we can speed up sample processing with little loss in data completeness as these spectra are removed in later stages in data processing workflows. DIDAR and the DIDAR GUI are compatible with all modern operating systems and are available at: . All files described in this study are available at as accession MSV000088887.
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影响因子：
7.4
作者：
Matzinger, Manuel;Mueller, Elisabeth;Duernberger, Gerhard;Pichler, Peter;Mechtler, Karl
通讯作者：
Mechtler, Karl
影响因子：
12.3
作者：
Specht H;Emmott E;Petelski AA;Huffman RG;Perlman DH;Serra M;Kharchenko P;Koller A;Slavov N
通讯作者：
Slavov N
影响因子：
3.3
作者：
Orsburn BC
通讯作者：
Orsburn BC
影响因子：
12.3
作者：
Budnik B;Levy E;Harmange G;Slavov N
通讯作者：
Slavov N
DOI：
10.1021/jasms.3c00240
发表时间：
2023-08-18
影响因子：
3.2
作者：
Sanchez-Avila, Ximena;Truong, Thy;Kelly, Ryan T. T.
通讯作者：
Kelly, Ryan T. T.