How to Determine the Number of Unique Peptides in MaxQuant Analysis Results?
MaxQuant is a widely used software for quantitative proteomics that processes mass spectrometry data to identify proteins and peptides.
In MaxQuant’s output files, information on unique peptides can be found in "peptides.txt," which contains detailed data for each identified peptide.
Each row in "peptides.txt" represents an identified peptide. The "Sequence" column lists the peptide’s amino acid sequence, the "Length" column specifies its length, and the "Modifications" column records any post-translational modifications.
The "Unique (Groups)" column designates whether a peptide is unique. A value of "+" in this column indicates a unique peptide, while a "-" signifies a non-unique peptide.
To determine the number of unique peptides, count the rows in which the "Unique (Groups)" column contains "+".
Note that the format and content of MaxQuant’s output may vary depending on the software version and settings. If the required information is not present in "peptides.txt" or if any issues arise, refer to the official MaxQuant documentation or contact technical support.
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider.
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