Tuesday, May 19, 2015

How to create multiconsensus reports in PD 2.0

This question has come up a couple of times so I figured I'd better cut a screenshot.  In old Proteome Discoverers we could open any MSF files we wanted by highlighting them and they would open as a "multiconsensus report".  There is a problem when we do this, however, we get no control over how it combines those files.

In PD 2.0 you can still create multiconsensus reports from your .MSF files but you must combine them into a .PDResult file and you have to do this through a new consensus step.

In the screenshot above I've opened one of the studies I've been messing around with.  (Please ignore all of the red exclamation points, I learned this software through trial and error...lots and lots of error!)  Anywho, if I highlight multiple .MSF files then when I click the Reprocess button my only option is the one above "use results to create new (multi) consensus report."  w00t!

When I do activate that I get this analysis pop up.

The processing steps that generated these MSF files are locked up. But you can go in and edit the consensus steps.  Things like how you deal with the quan and how many peptides per protein and FDR cutoffs can be set up the same between these files.  Since the Consensus steps are generally pretty rapid you get your final Consensus .pdresult file filtered tthe way you want them without waiting too long and everybody wins.


  1. Hi Ben! We are trying to do a multiconsensus in PD 2.1 like the one we used to do in PD 1.4. The problem we have is that in PD 1.4 the multiconsensus generate a few columns with data for each sample (score, coverage, # peptides, # PSM), but we don´t see these columns in PD 2.1, do you know is it is possible to generate it?
    Thank you! And thank you for your very nice blog and very useful videos.

  2. Hi Ben, i have the same identical problem. We do not see information about how each protein has been identified in each sample...i.e. how many peptides, PSMs, atc.
    Moreover I see that, when I do the Reprocess, The processing stesps also begin again and they are absolutely very slow.
    Have you a suggestion to solve these problems?