FlashLFQ's Settings

Coming soon.

General Settings

PPM Tolerance - the mass tolerance in parts per million for finding peaks in spectra corresponding to the input identifications. This is the mass tolerance for both MS/MS identified species and match-between-run species.

Normalize Intensities - This option tries to correct systematic bias introduced by instrument drift, sample preparation, etc. There are many types of normalization (see review 1, review 2). FlashLFQ uses a median-center normalization, which sets the the median peptide fold-change between any two samples to zero. The central assumption of this type of normalization (and most types of normalization) is that most proteins do not change in abundance between samples. If you expect most of your proteins to be changing in abundance, such as in certain types of pulldown experiments, then FlashLFQ's normalization may not be appropriate for your experiment. You may need to quantify peptides with FlashLFQ, normalize with separate software, and then re-import your quantitative results to FlashLFQ for statistical analysis. See the normalization page for more info.

Match Between Runs -

Use shared peptides for protein quantification -

Bayesian Protein Fold-Change Analysis -

Control Condition -

Fold-change cutoff -

Advanced Settings

Integrate Peak Areas

Only quantify identified charge

Require MS/MS identification in condition

Isotope PPM tolerance

Number of isotopes required

Maximum MBR window (minutes)

MCMC Iterations

MCMC Random Seed