I left a post here back in September mostly to remind myself to check out this software. Then I found that post while looking for a piece of software that does this. Who needs a memory? Not me!
THIS SOFTWARE IS CRAZY POWERFUL.
You can get it here.
Did you think the idea behind SIEVE from Vast (and later Thermo) was a great idea? Let's look at what is changing from one LC-MS run to the next -- and THEN let's try to ID those?
Did you also try SIEVE and wished it was: More stable, faster, more stable, had more features, was more customizable, more stable and didn't make you frightened to leave your 32-bit PC alone in your house when it was aligning big files?
MZMine is everything that SIEVE could have been. I can be mean about it now that it's been retired, right? Worth noting -- Compound Discoverer can do everything (and much more) that SIEVE could do -- for small molecules. It doesn't work well with peptides -- in my hands at least.
There are two downsides to MZMine that I've found already --
1) IT HAS TOO MUCH POWER.
2) IT GIVE YOU TOO MUCH OF THAT POWER
You can pick up most software for LFQ analysis and it will make a lot of useful assumptions for you. Like -- you'd like to align your peaks the one way it knows how to and you'd like to filter them in the one way it knows how to and you'd like to merge and filter them and it has a logical order for doing all those things.
In the MZMine your destiny is your own.
In MzMine -- you need to do some thinking -- maybe lots of thinking. You need to take your data and work through each step of processing it through. You appear to be able to do stuff that might not make sense at all. But you can always remove what you've just generated. I'm currently pressure testing that functionality.
Filtering? There's 5 of those. Peak detection? 8. Alignment? At least 3.
Once you develop your pipeline that isn't crazy at all you can build a batch mode to walk your data through all these steps. Okay -- I'll assume that's what you can do -- cause for all the attempts I've made for everything to turn out right Elizabeth is still being obstinate about Mr. Darby and Captain Bingsley seems like he'll never marry Lydia -- who was what? 14? Blech. What I mean is that nothing is working out in anywhere near the way I (or old Mr. Bennett) want it to.
Did I successfully interest you in checking out MZMine? Or did I just bring up half forgotten memories of creepy old books you had to read in 9th grade? If it's the former -- there's tons of documentation on MZMine. Here is the manual I just found. (PDF download) this is not a piece of software where you can succeed while randomly pushing buttons.