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CWRU-CPB / ProtMapMS

ProtMapMS is a search engine for protein footprinting experiments.
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Order of peptides in result files #3

Open rohitmpibpc opened 5 years ago

rohitmpibpc commented 5 years ago

Hi,

All the identified peptides with their values are mentioned in result table - identification/peak areas.

Could you tell about the reasoning behind their order ? It might help immensely to have them ordered with respect to starting residue ? For eg 309-330 is denoted first and then 309-335 and then 320-330.

Another issue is about repeat of peptides in peak area file. For e.g 309-330 is mentioned twice. First line has an empty R_1/0 Second line has some value. Could you explain the rationale ?

Thanks. Rohit

many-states commented 4 years ago

In the identification file, I see what you are saying. We may apply the sort you suggest in the next release, but in the meantime you could sort the spreadsheet on the start index column to achieve the same ordering.

The peak area file is listing peak areas extracted in each spectrum. The peptide appears once for each spectrum it was identified in, along with the corresponding peak area computed by integrating over the retention time interval. This is why it appears multiple times.