Neopeptide Analyser: A software tool for neopeptide discovery in proteomics data.
Neopeptide Analyser: A software tool for neopeptide discovery in proteomics data.
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DOI：
10.12688/wellcomeopenres.11275.1
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发表时间：
2017-04-07
影响因子：
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通讯作者：
Anderson J
中科院分区：
文献类型：
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作者：
Peffers M;Jones AR;McCabe A;Anderson J
基于质谱（MS）的蛋白质组学实验被广泛用于结缔组织的分析。常见的例子包括使用相对量化来识别软骨和肌腱中差异表达的肽和蛋白质。我们正致力于表征所谓的“新肽”，即由于蛋白质天然裂解而形成的肽，例如在病理条件下。与通常在MS工作流程中由于在体外使用酶（如胰蛋白酶）而定量的肽不同，新肽至少有一个末端不是由于在工作流程中使用胰蛋白酶而产生的。在这些数据集中鉴定新肽对于理解疾病病理学和开发抗体非常重要，这些抗体可以用作疾病（如骨关节炎）的诊断性生物标志物和新治疗靶点。我们之前描述的新多肽数据分析工作流程是费力的，并且不适合稳健的统计分析，这降低了对鉴定的新多肽的信心。为了克服这个问题，我们开发了“新肽分析仪”，这是一个用户友好的新肽分析工具，与无标记的质谱定量工具Progenesis QIP一起用于蛋白质组学。Neopeptide analyzer过滤来自Progenesis QIP输出的数据，以识别新肽序列，并在相应的蛋白质序列中给出与肽相邻的残基。它还为新肽量化值生成归一化值，并使用这些值执行统计测试，这些测试也包含在输出中。Neopeptide analyzer是一个Java应用程序，适用于Mac、Windows和Linux。分析功能和易用性鼓励数据探索，这可以帮助发现细胞外基质降解的新途径，识别潜在的生物标志物，并作为研究基质周转的工具。新肽分析仪可从https://github.com/PGB-LIV/neo-pep-tool/releases/获得。
Experiments involving mass spectrometry (MS)-based proteomics are widely used for analyses of connective tissues. Common examples include the use of relative quantification to identify differentially expressed peptides and proteins in cartilage and tendon. We are working on characterising so-called ‘neopeptides’, i.e. peptides formed due to native cleavage of proteins, for example under pathological conditions. Unlike peptides typically quantified in MS workflows due to the in vitro use of an enzyme such as trypsin, a neopeptide has at least one terminus that was not due to the use of trypsin in the workflow. The identification of neopeptides within these datasets is important in understanding disease pathology, and the development of antibodies that could be utilised as diagnostic biomarkers for diseases, such as osteoarthritis, and targets for novel treatments. Our previously described neopeptide data analysis workflow was laborious and was not amenable to robust statistical analysis, which reduced confidence in the neopeptides identified. To overcome this, we developed ‘Neopeptide Analyser’, a user friendly neopeptide analysis tool used in conjunction with label-free MS quantification tool Progenesis QIP for proteomics. Neopeptide Analyser filters data sourced from Progenesis QIP output to identify neopeptide sequences, as well as give the residues that are adjacent to the peptide in its corresponding protein sequence. It also produces normalised values for the neopeptide quantification values and uses these to perform statistical tests, which are also included in the output. Neopeptide Analyser is available as a Java application for Mac, Windows and Linux. The analysis features and ease of use encourages data exploration, which could aid the discovery of novel pathways in extracellular matrix degradation, the identification of potential biomarkers and as a tool to investigate matrix turnover. Neopeptide Analyser is available from https://github.com/PGB-LIV/neo-pep-tool/releases/.