PTMProphet result #331
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Dear Philosopher developers, The version of philosopher I'm using is 4.1.1, I notice there is no column Number of Phospho Sites in file psm.tsv now. If I want to know how many phosphorylation sites there are in this spectrum, should I get this information from column Assigned Modifications or column Modified Peptide? I found a few cases where these two columns don't exactly match. Looking forward to your reply.
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Replies: 1 comment
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Hi @XiaofengxBjmu There's a difference between knowing that a peptide is modified by a phosphorylation, for example, and having confidence where the localization is. The search engine can identify the modified peptide, and then PTMProphet will calculate a confidence score of the modification position. There will be cases where PTMProphet won't be able to reach the confidence threshold (i.e., above 75% probability), and so in these cases, the STY column will be empty. |
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Hi @XiaofengxBjmu There's a difference between knowing that a peptide is modified by a phosphorylation, for example, and having confidence where the localization is. The search engine can identify the modified peptide, and then PTMProphet will calculate a confidence score of the modification position. There will be cases where PTMProphet won't be able to reach the confidence threshold (i.e., above 75% probability), and so in these cases, the STY column will be empty.