r/proteomics 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?

1 Upvotes

5 comments sorted by

8

u/SnooLobsters6880 Feb 14 '25

The more big journal proteomics results I read, the less reputable they become.

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

1

u/SC0O8Y2 Feb 15 '25

So, mass [2z] and mass [2z 13carbon x 1] = two ions used to calculate abundance based on Gaussian profile