I'm a bigger fan of the MSAmanda algorithm than most people I run into. I still stick to my guns on this one, if I have to localize labile PTMs from HCD or CID fragmentation alone, I'm taking MSAmanda over just about everything else. The criticism I hear is that MSAmanda is slow. This criticism has gotten back to the developers because MSAmanda 2.0 is out of the shop and ready to go. (They changed the algorithm, I added the geography-appropriate racing stripes. The flames are from the tires shredding the pavement of PTM enriched Raw files!)
Quadrupole Orbitrap Plus RAW file; 2 hour gradient; 1ug of HeLa; 5ppm MS1; 0.02 Da MS/MS (roughly 19,000 PSMs)
SequestHT -- 11 min
MSAmanda -- 17 min
MSAmanda 2.0 -- 14 min
Wait...that isn't that much faster....is that 22%....deserving of racing stripes? Yes. Ask any 16 year old male. If you put a part on a car that improves that car's performance (or volume) by more than 1% you are now fully entitled to put racing stripes on that car.
Proof -- My spray paint can exterior car updates on my first car, post muffler delete! An example of the dumb stuff I did before I had internet access.
Check this out, though! MSAmanda allows for a load of dynamic mods! (24?!?!? This bears further testing!)
What if we search some PTM data?
I grabbed phosphotyrosine enriched data from a study just published in Nature Leukemia (more on that awesome study later!) and set up test #2:
Quadrupole Iontrap Orbitrap 2 hour gradient: 5ppm MS1; 0.02 Da MS/MS Dynamic phosphorylation (shown above)
MSAmanda 2.0 -- 12min 43 seconds
Get this -- Sequest HT -- 18 min 52 seconds!
And this is the point you go back to your awful clipart construction in PPT and you put flames on the search engine! I can get my increase in PTM localization (arrows on the 6 ions that show where your phosphorylation isn't!)...
...AND a 50% increase in speed over SequestHT? In a free node?
As always, you can get these nodes at PD-nodes.org
Disclaimer: I did run my tests for MSAmanda 1.0 in PD 2.1 and MSAmanda 2.0 in the beta version of PD 2.2
EDIT 7/4/17: How does MSAmanda 2.0 do with 46 data files (roughly 1,000,000 MS/MS spectra) vs. SequestHT?
MSAmanda 2.0 processed the files in 8 hr 27 min
Sequest HT processed the files in 6 hr 14 min
For straight peptide ID, MSAmanda 2.0 + Percolator is still not as fast as SequestHT. However, it is free!