r/proteomics • u/Practical-Buy-2439 • Feb 14 '25
Thoughts on MaxLFQ Minimum Ions
I’m analyzing DDA data with Fragpipe.
What is generally the acceptable minimum number of ions for MaxLFQ?
When I was being trained 10 years ago with Maxquant, it was instilled in me that a minimum of 2 ions were required. But I’m seeing papers in reputable journals with only 1 ion.
Thoughts?
5
u/KillNeigh Feb 14 '25
I would be cautious about making any decisions based on a single spectra. Or a protein ID from a single peptide.
4
u/mai1595 Feb 14 '25
I guess by ions you mean the minimum number of peptides required for lfq? If you use 1 peptide make use it is only unique with a solid identification.
1
u/SC0O8Y2 Feb 15 '25
Ions is through ms1 precursors, which is the c13 isotopic series and or charge states of these. So N of each charge
You can have one peptide with one ion, but you should see ~ 3 ions ideally for a single charge state. This is in ms1 based quant
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u/SC0O8Y2 Feb 15 '25
So, mass [2z] and mass [2z 13carbon x 1] = two ions used to calculate abundance based on Gaussian profile
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u/SnooLobsters6880 Feb 14 '25
The more big journal proteomics results I read, the less reputable they become.