After you have run a search and
assigned confidence to your identified PSMs, you can now calculate
relative quantification values for the proteins by running the
$ crux spectral-counts --threshold 0.1 --protein-database small-yeast.fasta ./crux-output/percolator.target.psms.txt
While the command is running, you will see output like this
INFO: Beginning spectral-counts. INFO: Total proteins found: 56 INFO: Assigning index 0 to ./crux-output/percolator.target.psms.txt. INFO: Number of matches:109 INFO: Number of matches passed the threshold 61 INFO: Number of peptides 15 INFO: Number of proteins 13
When the command is finished, it will print
INFO: Elapsed time: 0.0122 s INFO: Finished crux spectral-counts.
crux-output directory, there will be three new files:
The spectral-counts.target.txt file will look something like:
protein id NSAF YLR043C 0.61643416 YGL135W 0.17810018 YEL027W 0.10352074 YGL009C 0.035437137 YLR185W 0.031369921 YJR069C 0.014012959 YGR192C 0.0083149187 YMR235C 0.0067826854 YBR118W 0.0060274079
In this output, the first field is the identifier and the second field is the spectral-counting measure (NSAF, dNSAF, SIN, or EMPAI) result for each protein. To select which measure is computed, see the crux spectral-counts documentation.
Using peptideprophet probability from pepXML
crux spectral-counts also supports
using Peptide Prophet probabilities provided in a
pepXML file. Use the command:
$ crux spectral-counts --protein-database small-yeast.fasta --threshold-type custom --custom-threshold-name peptideprophet --threshold 0.9 --custom-threshold-min F target.pep.xml
Using mzIdentML files with spectral-counts
crux spectral-counts also supports mzIdentML as input. For example,
If the protein sequences are not provided within the given mzIdentML file, then you will have to provide a database using the protein-database parameter for the NSAF, dNSAF, EMPAI, and SIN metrics.