Calis-p Files

(C) Marc Strous, Xiaoli Dong and Manuel Kleiner, 2018, 2021

Usage:

java -jar Calisp-2.1.jar [options] -peptideFile [file_or_folder] -spectrumFile [file_or_folder]

General options:
-help                        print these instructions and exit.
-threads                     number of threads to use [default 4]. Speed ups may be observed up to 10 threads. Adding >10 threads may
                             not lead to more speed, as Calisp will become limited by reading mzML files from disk.
-spectrumFile                [.mzML] file or folder with [.mzML] file(s). If this is a folder, the source file(s) specified in the [.mzID]
                             file or [.target-peptide-spectrum-match] file must be identical to the source file specified in the [.mzML]
                             file. Alternatively, filenames (excluding extensions) must be identical.
-peptideFile                 search-engine-generated [.mzID] or [.target-peptide-spectrum-match] file or folder with these files.
-outputFile                  the name of the folder the output gets written to [default "calisp-output"].
-readIsotopeMatrixFile       read natural isotope abundances from this file instead of usig the default
-writeIsotopeMatrixFile      write default natural isotope abundances to this file, then exit

-keepMultipleOrganisms       peptides matching to multiple organisms will be included (by default they will be ignored)
-rejectMultipleProteins      peptides matching to multiple proteins will be ignored (by default they will be included)
-rejectSulfur                peptides containing cysteine or methionine will be ignored (by default they will be included)
-rejectModifications         peptides with post-translational modifications will be ignored (by default they will be included)

-organismDelimiter           for metagenomic data, the delimiter that separates the organism ID from
                             the protein ID [default "_"]. Use "-" to ignore organism ID entirely.
-isotope                     The target isotope. Valid options: 13C, 14C, 15N, 2H, 3H, 17O, 18O, 33S, 34S, 36S (default 13C).
-outputAllSpectra            Report each individual spectrum extracted. This is a very large file only useful for troubleshooting Calisp.

Examples:

To compute 13C content and delta13C of identified peptides in files within folder "my_peptide_folder" and spectra in 
files within folder "my_spectrum_folder":

>java -Xms10g -jar Calisp-2.1.jar -peptideFile my_peptide_folder -spectrumFile my_spectrum_folder

To compute 18O content of peptides in file "my_peptide_file" and spectra in "my_spectrum_file", ignoring organisms:

>java -jar Calisp-2.1.jar -isotope 18O -organismDelimiter - -peptideFile my_peptide_file -spectrumFile my_spectrum_file

Note that the argument "-Xms10g" is used to provide calisp with more memory, which will be needed for processing larger (>5) sets
of .mzML files.

More options for expert use are explained in the wiki (https://sourceforge.net/p/calis-p/wiki/Home/)