If you’re already using Progenesis LC-MS, you’ll know that it’s a very powerful piece of software. But are you using it to its fullest potential? And how much do you know about the quantification and statistics it uses? The knowledgebase and FAQs, available from the support section section of nonlinear.com, are full of documents that can help.
Here are the 3 most popular articles for LC-MS analysis:
- How do I use tags?
Tags are one of the most flexible analysis tools in Progenesis, allowing you to attach a label to a selection of features. You can then show or hide features using a filter that’s based on a selection of their tags. Tags really are a fundamental part of any investigation.
- P-values, False Discovery Rate (FDR) and q-values
In any analysis, it’s vital to understand the numbers. Progenesis LC-MS uses a range of statistical measures to help you draw meaningful conclusions from your experiments. This article focuses on the meaning and use of p-values and q-values.
- How does normalisation work in Progenesis LC-MS?
To be able to make valid comparisons across runs, protein and peptide abundances must be normalised. But how are the normalised values calculated? This article explains all. There’s also an article that further explains how normalisation is performed in multi-fraction experiments.
Of course, if you have any questions that aren’t answered by our support articles, please do let us know. Who knows; maybe your question will be made into a new FAQ of its own.