spectral mapping rate

[Ruben Bakker]

hello everyone, 

We have had low spectral identification rates of our files using MaxQuant or MetaMorpheus and therefore are now using Peptide-Shaker. However, I cannot find the spectral identification rate per file. I do have the output of peptide-shaker when loading the data of search-gui, I included the file in the conversation (html). 

It says: 

File import completed. 374973 first hits imported (3281204 total) from 405528 spectra.  [374385 first hits passed the initial filtering]

Could I simply conclude that 3281204 / 405528 * 100 ~ 80 % mapping rate (which seems extremely high). 

Thank you,

Ruben 

[Harald Barsnes]

Hi Ruben,

The identification rate per spectrum file can be found in the Spectrum IDs tab in PeptideShaker after the data has been processed. With regards to the first hits imported, this number is before the statistical validation, hence it will drop significantly.

Best regards,

Harald

[Ruben Bakker]

Hi Harald, 

Thank you for your response, it is very helpful! If we were to run peptide-shaker from the terminal; in what type of report do we find the identification rate per spectrum file or do we have to use the GUI? Similar information is printed to the command line either reading in the data using a gui or command line tool. 

Best regards,

Ruben

[Harald Barsnes]

Hi Ruben,

I'm afraid that not all of the information in the Spectrum IDs tab is directly available via the command lines, but you may be able to get the information you want from the some of the reports. The easiest option is perhaps to use the Certificate of Analysis export and look at the #Validated PSM field? 

Note that if the default reports do not contain the information required, you can also set up your custom reports and use those via the command line.

Best regards,

Harald

[Ruben Bakker]

Thank you for your explanations Harald! 

Best regards,

Ruben