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Wang-kaifei / DBReducer

A universal database reduction method based on the sequence tag strategy to facilitate large-scale database search in proteomics
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结果文件的解读？ #1

Open BinhongLiu opened 1 year ago

BinhongLiu commented 1 year ago

王老师您好， 我是初次接触到蛋白组学数据分析和处理，刚刚测试了您的流程，可以成功跑通，但是对分析产生的结果文件不是特别的解读准确。我自建了一个短肽的数据库（长度从10-100氨基酸），通过和蛋白质组样本比对，想找出数据库中哪些短肽在样本中出现。分析结果中的DBReducer.fasta文件就是这个问题的答案么？另外，其他结果文件应该如何解读，都保存着哪些结果内容？ 谢谢您的解答。 image

Wang-kaifei commented 1 year ago

Dear,

Sorry for not noticing your question due to the previous email deactivation.

I understand your question is that you want to know which peptides in the database appear in the sample data, which belongs to the problem of peptide identification. I recommend you to use pFind software (http://pfind.org/software/pFind/index.html) to search.

DBReducer software, a database reduction tool, is suitable for reducing large databases in application scenarios such as metaproteomics and proteogenomics to a more precise database to bridge subsequent refinement search. That is, the end result is a smaller fasta file.

The pFind software provides the user interface and if you have any questions about the pFind software, you are also welcome to contact email: support@pfind.org.

In addition, there is an important update to the DBReducer software, if you continue to use it please download the latest version from http://pfind.org/software/DBReducer/index.html.

Best, Kaifei

BinhongLiu commented 1 year ago

Thanks for your reply! I understand that the DBReducer.fasta file is the reduced database, and files prefixed by "pFind" are the result files of the pFind software. Among these result files, pFind.protein is the file that contains the peptides appearing in the sample data and is just what I'm looking for, right? Thanks!

Wang-kaifei commented 1 year ago

Dear Binhong,

If you need regular protein identification and want to know which peptides are present in your samples, we recommend you use pFind software directly.

The focus of DBReducer is different from that of pFind. DBReducer is mainly designed for the application of large databases, such as proteogenomics or metaproteomics. The identification results obtained by DBReducer are not recommended to be the final results, and it is better to connect to another search against the reduced database.

Best, Kaifei