Hello,

I've been trying to use the IsoCorrectoR package to correct and calculate the mean enrichment for 15N-labeled peptide data. It mostly works beautifully, but I found that it throws an error for larger peptides in the MolculeFile. I was able to pinpoint that it works for molecules with elemental formulas that have 170 or fewer H atoms, but errors when there are 171 or more H atoms. After a bit of testing, it appears that high C atom abundance (>= 171) can also cause the error, but it appears to be insensitive to high O atom abundance.

I've been unsuccessful in trying to identify where in the code this error is originating, but hoped you might have a better idea. The error is: Error in if (icpms[["ProbIsoComb"]] > CalculationThreshold) { : missing value where TRUE/FALSE needed

Thanks very much, Amy

Example molecules that cause this error (no error occurs for these molecules when the H atom abundance is changed to 170): FLAFLVASENQGGYAAANHEYPLK,C121H174O34N30LabN30, SDVQGLYLDTTSmSSLEGYFASGELR,C122H186O45N30S1LabN30, TGNFTNSAFGFSASSGLYDALSGGTFATASGLEVAFEEGPK,C181H262O62N44LabN44,

Dear Amy,

many thanks for your detailed bug report. We'll have a look and fix it asap.

Kind Regards Christian

Dear Amy,

we have looked into the issue and fixed it. Use of IsoCorrectoR was initially intended for only small molecules (i.e., metabolites), so its internals were not built for and not tested for handling larger molecules like peptides or proteins. This is because of the internal calculation of the factorials needed to compute the probabilities the correction is based on. As I've discovered now, factorials of numbers larger than 170 will not work in R, numbers get too big. This results in this apparently arbitrary threshold of 170 that you observed.

We now solved the issue using log-space factorials. Your example peptides that originally produced the error run fine with the updated code on our test system. It may however take some time until the update is available in Bioconductor.

We are sorry for the inconvenience, and thank you for reporting the issue!

Kind regards,

Paul

Dear Amy,

please find the fixed versions of IsoCorrectoR here:

o v1.6.2 (current release 3.11)

o v1.7.2 (devel)

If you encounter further problems, please let us know.

Thanks again for helping us to improve the IsoCorrectoR package.

Cheers Paul and Christian