peak alignment and quantification software

[jonmike.reed]

Hello. Are there any freely-available programs that compare LC-MS runs (high resolution (100,000)) in full scan mode without regard to the analyte(s) of interest?

Essentially, we would like to use this approach for several of the various "-omic" approaches as a way to identify differentially-expressed molecules in a complex mixture, and go back later for targeted MSn characterization from a specified mass list rather than performing quantification via a BIG5 or some other DDA approach.

Any thoughts would be appreciated. Thanks.

[Gaetan Glauser]

XCMS can perform peak detection, integration, re-alignment, etc. as well as a little bit of multivariate analysis. There is an online version that is very user-friendly. Worth a try.

https://xcmsonline.scripps.edu/

The "real" software version works under R environment.

[lmh]

and R is free and fairly easy to set up, and you don't need to know much about R in order to run xcms.

If you do decide to install R, it will also handle PCA for you (and if you're feeling clever it can do PLS too).