State Key Laboratory of Microbial Metabolism (Shanghai Jiao Tong University) and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Protein Cell. 2012 Feb;3(2):140-7. doi: 10.1007/s13238-011-1129-8. Epub 2012 Jan 9.
Biologically important proteins related to membrane receptors, signal transduction, regulation, transcription, and translation are usually low in abundance and identified with low probability in mass spectroscopy (MS)-based analyses. Most valuable proteomics information on them were hitherto discarded due to the application of excessively strict data filtering for accurate identification. In this study, we present a staged-probability strategy for assessing proteomic data for potential functionally important protein clues. MS-based protein identifications from the second (L2) and third (L3) layers of the cascade affinity fractionation using the Trans-Proteomic Pipeline software were classified into three probability stages as 1.00-0.95, 0.95-0.50, and 0.50-0.20 according to their distinctive identification correctness rates (i.e. 100%-95%, 95%-50%, and 50%-20%, respectively). We found large data volumes and more functionally important proteins located at the previously unacceptable lower probability stages of 0.95-0.50 and 0.50-0.20 with acceptable correctness rate. More importantly, low probability proteins in L2 were verified to exist in L3. Together with some MS spectrogram examples, comparisons of protein identifications of L2 and L3 demonstrated that the staged-probability strategy could more adequately present both quantity and quality of proteomic information, especially for researches involving biomarker discovery and novel therapeutic target screening.
与膜受体、信号转导、调控、转录和翻译相关的生物重要蛋白质通常丰度较低，在基于质谱 (MS) 的分析中鉴定的可能性较低。由于对准确鉴定应用了过于严格的数据过滤，迄今为止，关于它们的大多数有价值的蛋白质组学信息都被丢弃了。在这项研究中，我们提出了一种分阶段概率策略，用于评估潜在功能重要蛋白质线索的蛋白质组学数据。使用 Trans-Proteomic Pipeline 软件从级联亲和分级的第二 (L2) 和第三 (L3) 层进行基于 MS 的蛋白质鉴定，根据其独特的鉴定正确率（即 100%-95%、95%-50%和 50%-20%），分为三个概率阶段：1.00-0.95、0.95-0.50 和 0.50-0.20。我们发现大量数据量和更多功能重要的蛋白质位于以前不可接受的低概率阶段 0.95-0.50 和 0.50-0.20，其正确性率可接受。更重要的是，L2 中的低概率蛋白质被证实存在于 L3 中。结合一些 MS 光谱示例，对 L2 和 L3 的蛋白质鉴定进行比较表明，分阶段概率策略可以更充分地呈现蛋白质组学信息的数量和质量，特别是对于涉及生物标志物发现和新型治疗靶点筛选的研究。
