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MaxQuant - second peptide search

I'm trying MaxQuant for trial data. Our data consists of 35 samples (15 controls and 20 diseased samples). Each file size is ~4.8Gbs.

We changed the parameters in mqpar.xml (file attached) according to the experimental setup.

Maxquant ran for around 2 days and the disk space ran out (~7 Tbs). When we checked log, the last step it was undergoing is 'Second peptide Search'.

Does second peptide search create huge intermediate files and takes this much time? And is 'second peptide search' really necessary for MS data processing?

peptide-search proteome maxquant
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updated by douwevanderleest 2 • | written by anu014 19

I just experienced the same thing with a little less disk space. I ran version maxquant_v2.7.5.0. Do you know if there is an update on it's way or is this otherwise an issue that just needs lots and lots of disk space?

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written by douwevanderleest 2

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