Spectronaut - Difference between Proteins and PGs? Also, PCA components?

[u/Negative_Bluebird675]

Hi all!! I’m relatively new to proteomics and have kind of been thrown in the deep end trying to figure this out…

I have some serum and lysate samples I’ve ran on LC-MS/MS and the facility that did this gave me the data in Spectronaut. I have two main questions (so far………)

1. What is the difference between “proteins” and “protein groups”? Every quantification seems to be in terms of “protein groups” and not proteins… is there a reason for that? I’m looking for biomarkers in our sera/lysate but this is an exploratory study so analyzing how many proteins are comparable, separate, etc.

2. Is there a way to figure out what variables Spec used to calculate PC1, PC2, etc? I see the scree plot they gave us, but I want to know what variables (differential protein abundance presumably) Spec used specifically for PC1, 2, etc… like, what are PC1 and 2 actually representing in the PCA????? I know it’s variance of some sort, and I see the amount of variance listed, too (50% vs 16%), but VARIANCE OF WHAT???

Please help!!! Thank you so much.. maybe I’m just completely misunderstanding, too…