I am using MaxQuant to analyze some label-free experiment data. I did an affinity chromatography experiment and I have a technical triplicate of the elution and a technical triplicate of the flowthrough. I am interested only in the peptides and the (aggregated) intensity columns in the peptides.txt file for downstream analysis. I ran the program twice (once with each of the following configurations) and I'm trying to understand the slight differences to make sure I'm doing the right thing. The peptides are the same but the Intensity of some peptides is slightly different. I couldn't find a good guide about the experimental design. I appreciate any assistance. If you think there might be better settings for this analysis, please feel free to share!
Configuration 1: Experiment | Fraction a | 1 a | 2 a | 3 b | 4 b | 5 b | 6 Configuration 2: Parameter Group |Experiment | Fraction | a | 1 b | 1 c | 1 d | 1 e | 1 f | 1 Thanks!
Please look at the following below links which may help you in your analysis:
https://pharmazie.uni-greifswald.de/storages/uni-greifswald/fakultaet/mnf/pharma/biotechno/dokumente/MaxQuant_Infos_and_Tutorial_07.pdf
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6495250/pdf/zjw982.pdf
Thanks
Thanks for the reference Isam. I already did look at it but it is still not clear what is the actual difference between the 2 configurations. If you had any additional insight it will be very helpful!
- Badges
- Science topic
- Similar topics
- Filing