I tried MQ 220.127.116.11 for LFQ analysis and I noticed that there are different parameters to define the LFQ compared to older versions:
1. Global parameters in LFQ tab- top N peptides is set to 0 as a default (In older versions top N peptide didn’t appear). Is that default correct?
2. Group specific parameters – LFQ – Normalization type – can choose classic or none – what is the difference and what should I choose as default?
I analyzed same files in MQ18.104.22.168 (using default LFQ parameters) and MQ1.6.5 and got very different LFQ results.
All samples with LFQ had the same total protein IDs number
The LFQ Intensity Vs Intensity (left)seemed to be shifted (didn’t happened in MQ1.6.5, right side). May that be related to MQ 22.214.171.124 LFQ parameters?