蛋白质组学后搜索算法
Scavager的Python项目详细描述
scavager-蛋白质组学搜索后验证工具
脚本的基本操作需要.pep.xml或.mzid文件。当前支持的搜索引擎: 身份,X!串联,彗星,msfragger,msgf+,睡眠。
.fasta文件用于计算nsaf(无标签定量指数)、蛋白质序列覆盖率和氨基酸统计。
对于msgf+和morpheus搜索引擎,最好提供用于搜索的切割规则(这些搜索引擎不报告缺失的肽切割数量)。
scavager的输出包含:
tab-separated table with unfiltered peptide-spectrum matches (ends with _PSMs_full.tsv)
tab-separated table with identified peptide-spectrum matches at 1% PSM FDR (ends with _PSMs.tsv)
tab-separated table with identified peptides at 1% peptide FDR (ends with _peptides.tsv)
tab-separated table with identified proteins without grouping at 1% protein FDR (ends with _proteins.tsv)
tab-separated table with identified protein groups at 1% protein FDR (ends with _protein_groups.tsv)
png figure with PSM, peptide and protein features distributions
安装
使用PIP:
pip install Scavager
用法
可以使用以下命令运行算法(适用于python2.7/python3+):
scavager path_to_pepXML/MZID
OR
scavager -h
链接
- Bitbucket回购和发行跟踪程序:https://bitbucket.org/markmipt/scavager
- 邮件列表:pyteomics@googlegroups.com,markmipt@gmail.com