We wish to reach out to other proteomic scientists who are using Progenesis software for label-free quantitation. If people are also performing quantitative PTM analyses (e.g. phospho but limited to this), we would want to know how they are handling/manipulating their data and with which post-processing platforms.
Hey!
I know a group from Max Planck Institute for Molecular Plant Physiology that is using Progenesis on a daily basis for the label-free quantitation. I can send you the details on private if you are interested and nobody else will answer you.
Greets.
I have used it for several projects and am happy to provide details privately.
We are using Progenesis for phosphopeptide quantitation. we have published the outcome of that type of analysis few times (more similar work in the pipeline). I suggest that you check first how reproducible is your phosphoenrichment platform (ie you perform 3-4 independent phosphoenrichment from the same sample). And you optimise the process to ensure it is reproducible. I suggest that you assess both the enrichment and the LC-MS reproducibility. We are working on a tool that combine output from Progenesis and Maxquant to generate a more meaningful and concise output.
good luck
Thierry
Hi All, I was wondering what is the best scale to use for the Label-free quantitative data. Do you recommend using the normalized abundance directly or is it advisable to use a log scale value. Log 2 or Log 10
Thanks for any help
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