When can you use (or cannot use) Match between runs in MaxQuant?

No golden rule here. For quantitative comparison of different sample groups it can be valuable to use MBR to increase the number of identified + quantified proteins in all samples and then have more proteins that occur in most of the samples to compare them.

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{% snippet  topics/proteomics/tutorials/maxquant-msstats-dda-lfq/faqs/match.md %}

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