PepOSX-Exhaust User Guide
A lightweight and efficient algorithm for identification of short peptides
PeposX-Exhaust is a lightweight, open-source tool written in Python that is designed to analyze the short peptides in food-derived protein hydrolysates and ferments. The tool is free for use and is expected to help advance the development of peptidomics by providing researchers with a simple and efficient way to characterize the peptide composition of short peptides in these products.
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PeposX-Exhaust是一款用python语言编写的轻量级、开源肽组学分析工具，该工具可用于分析食品或生物来源蛋白质水解物和发酵产物中的短肽。该工具可免费使用，并希望通过为研究人员提供一种简单高效的肽组学分析方法，来帮助推进多肽组学的发展。
Figure 1. Overview of workflow of PeposX-Exhaust
图1. PeposX-Exhaust运行流程概览图
Procedure
1. Support Device Environment (支持设备环境):
1.1 Computer System: Windows 10 and above.
1.2 Do not use software such as VPN.
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1.1计算机系统：windows10及以上版本。
1.2 请勿使用VPN等这类软件。
2. App installation(应用程序下载):
2.1 Locate the "Download" button in the upper left corner of this page.
2.2 Click the "Download" button.
2.3 Specify the file saving path and click "Save".
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2.1找到页面左上角的“下载”按钮。
2.2点击“下载”按钮。
2.3指定文件保存路径，点击“保存”。
3. Workflow(工作流程):
3.1 Unzip the downloaded package.
3.2 Open the ‘PeposX-Exhaust’ folder and locate ‘MainEngine.exe’(Figure 2).
3.3 Make sure your computer is connected to the internet.
3.4 Double-click ‘MainEngine.exe’.
3.5 Determine if the free use period is still active. If it is, proceed to Step 3.6. If it is not, proceed to Step 3.7.
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3.1解压下载文件。
3.2打开“PeposX-Exhaust”文件夹，找到“MainEngine.exe”(图2)。
3.3确保你的电脑连接到互联网。
3.4双击“MainEngine.exe”。
3.5验证软件是否处于免费使用期。如果是，开始步骤3.6。如果不是，请查看步骤3.7。
Figure 2. ‘MainEngine.exe’ location in the ‘PeposX-Exhaust’ folder
图2. ‘MainEngine.exe’应用程序在‘PeposX-Exhaust’ 文件夹的位置
3.6 Start setting parameters. See Figure 3 and Figure 4 for reference.
3.6.1 Convert multi-charged precursor ions into single-charged ions (reference value: y/n)
3.6.2 Coverage rate of fragment ions (reference value: Number)
3.6.3 Intensity threshold of precursor ions (reference value: Number)
3.6.4 Use monoisotopic masses (0) or average mass (1) (reference value: 0/1)
3.6.5 Input the precursor tolerance error (Da) (reference value: Number)
3.6.6 Input the fragment tolerance error (Da) (reference value: Number)
3.6.7 Input the minimum length of sequences (reference value: Recommend≥2)
3.6.8 Input the maximum length of sequences (reference value: Recommend<9)
3.6.9 Input the number of cores (reference value: No more than the number of cores equipped with the computer)
3.6.10 Input ion series (reference value: a,b and(or)y)
3.6.11 Distinguish isoleucine (I) and leucine (L) (reference value: y/n)
3.6.12 Input the path or directory of the files (reference value: directory where the file is located)
3.6.13 Use fasta file for peptide sequencing (reference value: y/n)
·If ‘y’ is entered, proceed to Step 3.6.14(Figure 3). If ‘n’ is entered, proceed to Step 3.6.15(Figure 4).
3.6.14 Input the path or directory of the fasta file (reference value: including the suffix)
3.6.15 Use for batch processing (reference value: y/n)
·If ‘y’ is entered, proceed to Step 3.6.17. If ‘n’ is entered, proceed to Step 3.6.16.
3.6.16 Input the full name of the mgf format file (reference value: including the suffix)
3.6.17 start identification
3.7 Contact the author to obtain free permission.
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3.6开始设置运行参数。参考图3和图4。
3.6.1将多电荷前体离子转化为单电荷离子(输入参考值:y/n)
3.6.2碎片离子覆盖率(输入参考值:数值)
3.6.3前体离子强度阈值(输入参考值: 数值)
3.6.4使用单同位素质量(0)或平均质量(1)(输入参考值:0/1)
3.6.5输入前体离子容错值(Da)(输入参考值:数值)
3.6.6输入片段离子容错值(Da)(输入参考值:数值)
3.6.7输入最小序列长度(输入参考值:建议≥2)
3.6.8输入最大序列长度(输入参考值:推荐<9)
3.6.9输入核心数(输入参考值:不超过计算机配备的核心数)
3.6.10输入离子簇(输入参考值:a、b和(或)y)
3.6.11区分异亮氨酸(I)和亮氨酸(L)(输入参考值:y/n)
3.6.12输入文件所在路径或目录(输入参考值:文件所在目录)
3.6.13使用fasta文件进行肽段测序?(输入参考值:y/n)
·如果输入“y”，继续执行步骤3.6.14（图3）。如果输入“n”，请继续执行步骤3.6.15（图4）。
3.6.14输入fasta文件的路径或目录(输入参考值:包含文件后缀)
3.6.15用于批量处理?(输入参考值:y/n)
·如果输入“y”，继续执行步骤3.6.17。如果输入n，执行步骤3.6.16。
3.6.16输入maf格式文件的全称(输入参考值:包括文件后缀)。
3.6.17 开始鉴定
3.7联系作者获取免费许可使用。
Figure 3. Software setup parameters (using the fasta sequence library)
Figure 3. 软件设置参数（使用fasta序列库）
Figure 4. Software setup parameters (do not use the fasta sequence library)
图 4. 软件设置参数（不使用fasta序列库）
4. Run the software and check the identification result. (软件运行与结果查看):
4.1 Start the short peptide identification operation.(Figure 5)
4.2 Once the analysis is complete, a message will be displayed.(Figure 6)
4.3 The identification result will be saved in the directory where the original data is stored.(Figure 7)
4.4 The identification results can be viewed by software such as Excel.(Figure 8)
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4.1 开始短肽鉴定操作。（图5）
4.2 当分析结束后，输出信息提示。（图6）
4.3 鉴定结果保存在原始文件所在目录下。（图7）
4.4 鉴定结果可以使用excel等软件查看。（图8）
Figure 5. Start the short peptide identification operation
图 5.开始短肽鉴定操作
Figure 6. Complete the identification
图 6.完成鉴定
Figure 7. The identification result will be saved in the directory where the original data is stored
图 7. 鉴定结果保存在原始文件所在目录下
Figure 8. The identification results can be viewed by Excel
图 8. 鉴定结果可以通过Excel查看
Note
The current version of the software is for use in the publication stage of paper, it is free for one year. If you experience issues during the free period, it may be due to a network problem, please contact us for assistance. The software will be available for free to all users in the future.
软件可免费使用一年，如您在免费使用期间遇到问题，请注意首先检查您的网络连接情况。如需要帮助，亦可联系我们（xujucai.happy@163.com）。该软件将持续在未来免费提供给所有科研用户。