![]() ![]() ![]() Since you may not have such computational resources to perform 6 searches per mass spec sample, you may want to know individual performance. Their results show that you get maximum IDs when you search with all these programs. Many people are familiar with these search programs. They tested combination of multiple engines including SEQUEST, Inspect, X!tandem, MASCOT, Myrimatch and OMSSA. According to David Shteynberg’s paper (MCP 12.9, 2013, 2383-2393), the more engines you add, the more IDs you get even at strict false discovery rate. If you have unlimited computer resources, you can use as many as search engines you want. If you have access to cloud computer or cluster, you will get your searches done quickly. Sample prep for mass spec is time consuming and costly, while computation is getting faster and faster. Well known sequence search engines such as SEQUEST, X!tandem, MSGF+ and Myrimatch are based on searching against theoretical fragmentation of peptide generated from sequence database, so they are belong to 1). First, the search programs for mass spec can be categorized into 3 kinds.ġ) Search against protein sequence database In this post I am going to discuss about how to maximize IDs using multiple search programs. There are quite a few search engines out there but using all of them seem to be unreasonable. I have posted a few times regarding multiple search engines to increase PSMs (peptide spectrum matches).
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