Issue 60: Import transition list can pick unlikely ions when more likely ions are with m/z match tolerance

Assigned To:Guest
Opened:2011-07-07 by Brendan MacLean
Changed:2013-08-09 by Brendan MacLean
Resolved:2013-08-09 by Brendan MacLean
Closed:2013-08-09 by Brendan MacLean
2011-07-07 Brendan MacLean
Title»Import transition list can pick unlikely ions when more likely ions are with m/z match tolerance
Assigned To»Brendan MacLean
Hi Brendan,

When optimizing peptides using Agilent's Peptide Optimizer software the output only has 1 decimal place. If I create a transition list from these masses to import into Skyline, Skyline tries to match the masses as accurately as it can with any products...including c,x and z ions. I can't seem to over ride this by choosing only y and b ions in the transition settings parameters, or tightening up the ion match tolerences. How can I force Skyline to assign only y and b ions to my Agilent transition list?



2010-12-08    Brendan
Hi Angela,
You are going to have to give me a transition list example that is getting the wrong ions assigned. Skyline does test for all possible ions, but it should start with the Y and B ions. That means you shouldn't see the other types unless, your product m/z values fail to match a Y or B ion. In fact, reducing the match tolerance could make this worse. You would need at least a .055 tolerance to allow everything rounded to a single decimal place to get matched to its proper Y or B ion. Once it fails to match Y or B, then it will start looking at other options.

I certainly could have gotten it wrong in some case. If you have an example where you are not getting what you want, please post it to this issue report, and maybe post the .sky file you are starting with also (using Attach a file).

Thanks. I am sure we can figure it out.


2010-12-09    Angela
Hi Brendan,

I've attached a small .sky file where I had the transition setting set to y ions only. Because Agilent's Optimizer software automatically creates a results file with the product ion m/z accurate to one decimal place, Skyline is forced to match these values to all the possible product ions for that peptide. Skyline does a great job and matches the product ion with the closest m/z but sometimes it chooses a c,x or z ion or possibly a higher charge state y ion. I would like to over ride this by limiting it to y ions with a single charge in the transition settings tab but I can't seem to. Is it possible to over ride this some other way?

 top 5 transition list for skyline_group
 top 5 transition list FROM skyline_20101202_group 04_K8.csv

2010-12-10    Brendan
Hmmm... I see. I did change the algorithm a while ago to use the closest ion, at a request from another user, from its original implementation, which searched ions in order, and used the first match it found. That would probably work for you, but it had its own issues. I'll have to give this a little more thought to be able to make everyone happy.

In the meantime, it might be worth checking out the optimization functionality in Skyline. I have been told it compares favorably with Optimizer.

2013-08-09 Brendan MacLean
resolve as Fixed
Fixed in r4574

2013-08-09 Brendan MacLean
Assigned ToBrendan MacLean»Guest