Isoformer tool [Download versions for WINDOWS or MAC] - available here soon!
When working with a group of proteins of very similar sequence (polymorphic isoforms within a species or the same protein from multiple species, it can be tedious identifying unique or common peptides that would allow quantification using stable isotope labelled peptides (or QconCATs). I therefore wrote Isoformer.
Isoformer accepts a simple fast file of all relevant proteins, and then, given the protease to be used, and restricting peptides on the basis of mass, the presence of deamidating NG sequences (a pain for quantification), ir generates a simple tab delimited file of unique peptides and their presence in each protein sequence.
Please note that this is not even a beta version yet, but the core functionality works for me. I will put the executables up as soon as I can.
My goal is to eventually allow the user to highlight specific peptides and say 'build me the QconCAT sequence'.
The Windows or Mac versions of the software are downloadable here as zip files that will expand to a stand alone application. Note that your browser might complain about a safe download. Any issues, email me.
When working with a group of proteins of very similar sequence (polymorphic isoforms within a species or the same protein from multiple species, it can be tedious identifying unique or common peptides that would allow quantification using stable isotope labelled peptides (or QconCATs). I therefore wrote Isoformer.
Isoformer accepts a simple fast file of all relevant proteins, and then, given the protease to be used, and restricting peptides on the basis of mass, the presence of deamidating NG sequences (a pain for quantification), ir generates a simple tab delimited file of unique peptides and their presence in each protein sequence.
Please note that this is not even a beta version yet, but the core functionality works for me. I will put the executables up as soon as I can.
My goal is to eventually allow the user to highlight specific peptides and say 'build me the QconCAT sequence'.
The Windows or Mac versions of the software are downloadable here as zip files that will expand to a stand alone application. Note that your browser might complain about a safe download. Any issues, email me.
