Department of Communications Engineering, University of the Basque Country (UPV/EHU), Alda, Urquijo s/n, Bilbao, 48013, Spain.
BMC Bioinformatics. 2012 Nov 5;13:288. doi: 10.1186/1471-2105-13-288.
Protein inference from peptide identifications in shotgun proteomics must deal with ambiguities that arise due to the presence of peptides shared between different proteins, which is common in higher eukaryotes. Recently data independent acquisition (DIA) approaches have emerged as an alternative to the traditional data dependent acquisition (DDA) in shotgun proteomics experiments. MSE is the term used to name one of the DIA approaches used in QTOF instruments. MSE data require specialized software to process acquired spectra and to perform peptide and protein identifications. However the software available at the moment does not group the identified proteins in a transparent way by taking into account peptide evidence categories. Furthermore the inspection, comparison and report of the obtained results require tedious manual intervention. Here we report a software tool to address these limitations for MSE data.
In this paper we present PAnalyzer, a software tool focused on the protein inference process of shotgun proteomics. Our approach considers all the identified proteins and groups them when necessary indicating their confidence using different evidence categories. PAnalyzer can read protein identification files in the XML output format of the ProteinLynx Global Server (PLGS) software provided by Waters Corporation for their MSE data, and also in the mzIdentML format recently standardized by HUPO-PSI. Multiple files can also be read simultaneously and are considered as technical replicates. Results are saved to CSV, HTML and mzIdentML (in the case of a single mzIdentML input file) files. An MSE analysis of a real sample is presented to compare the results of PAnalyzer and ProteinLynx Global Server.
We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool.
在 shotgun 蛋白质组学中，从肽鉴定推断蛋白质时必须处理由于不同蛋白质之间存在共享肽而产生的歧义，这在高等真核生物中很常见。最近，数据独立采集 (DIA) 方法已成为 shotgun 蛋白质组学实验中传统数据依赖采集 (DDA) 的替代方法。MSE 是用于命名 QTOF 仪器中使用的 DIA 方法之一的术语。MSE 数据需要专门的软件来处理采集的光谱并执行肽和蛋白质鉴定。然而，目前可用的软件没有考虑肽证据类别，以透明的方式将鉴定的蛋白质分组。此外，获得的结果的检查、比较和报告需要繁琐的手动干预。在这里，我们报告了一种软件工具，用于解决 MSE 数据的这些限制。
在本文中，我们介绍了 PAnalyzer，这是一种专注于 shotgun 蛋白质组学蛋白质推断过程的软件工具。我们的方法考虑了所有鉴定的蛋白质，并在必要时使用不同的证据类别对其进行分组并指示其置信度。PAnalyzer 可以读取 Waters 公司提供的 ProteinLynx Global Server (PLGS) 软件的 XML 输出格式的蛋白质鉴定文件，以及最近由 HUPO-PSI 标准化的 mzIdentML 格式。也可以同时读取多个文件，并将其视为技术重复。结果保存到 CSV、HTML 和 mzIdentML（在单个 mzIdentML 输入文件的情况下）文件中。还呈现了一个真实样品的 MSE 分析，以比较 PAnalyzer 和 ProteinLynx Global Server 的结果。
我们提出了一种软件工具来处理蛋白质推断过程中出现的歧义。主要贡献是支持 ProteinLynx Global Server 的 MSE 数据分析和技术重复集成。PAnalyzer 是一个易于使用的跨平台免费软件工具。
