You summarised my entire semester of listening to droning lectures. I don't know why we don't have more effective teaching in schools. THIS WAS SO MUCH BETTER.
Thank you, I'm glad you found it helpful. It was one of those topics that had me thinking "am I really the right person to cover this", but it has ended up being one of my most successful videos!
Thanks, yes it was really an exercise in prioritization. I had to cut things like DDA vs. DIA as well as SWATH, both of which would have required major detours to fit in. They are probably topics that should be covered in a "deeper dive" presentation later.
Thank you for the excellent presentation Professor. I have a question if you could answer or link to another video of you would be greatful. What are the different types of proteomics quantification methods? 1. Does it always LC-MSMS data analysis use peak area of XIC for quantification? Is isn’t possible to use peak intensity values? 2. In Label Free Quantification (LFQ / MaxQuant) what does it use ? What is the mechanism behind this?
I'm not completely sure what you mean. To do quantification you need to integrate the peak intensity, which in turn requires detecting where the peaks start and end. XIC is the most common peak detection algorithm as far as I know. I'm sure you can use other peak-detection algorithms than XIC, but I don't think you can avoid detecting peaks and integrating the area under them. Regarding LFQ in MaxQuant, the algorithm is called MaxLFQ - explaining it would take an entire paper (pubmed.ncbi.nlm.nih.gov/24942700/).
It should be the proteinGroups.txt that contains the identified proteins (or rather protein groups) and the intensity for each of them in each sample. Those are the values you need as input for a statistical analysis to identify differentially expressed proteins.
can someone explain what does the peak intensity mean? it is the number of ions we measure that have the same m/z ratio? How do we use this information? Also, does it relate with the term 'base peaks'?
Yes, pretty much. Peak intensity is not the number of ions itself, but it should be proportional to the abundance of ions at the m/z ratio. The base peak in a spectrum is simply the most intense peak, and peak intensities are thus commonly normalized so that the base peak intensity is 100%.
I'm the wrong person to ask. While I'm a bioinformatician and work with many types of proteomics data, I'm not an expert on the many technologies. So I cannot tell you which upcoming technologies are likely to be successful and which are not.
Aside from the references to where figures are from, I unfortunately do not have them. This overview was simply based on what I know - I do not know where I know each thing from, and digging up references for it would be equivalent to doing the work for writing a review article on the topic.
I was not thinking of SWATH, although SWATH is compatible with multiplexing (as far as I know). What I had in mind was labeling approaches such as iTRAQ and TMT, which allow you to multiplex 8 and 16 samples respectively.
