-h [ --help ]
Print the help message.
-a [ --activation ] <CID|HCD|ETD|UVPD|FILE>
Set the fragmentation method(s) of MS/MS spectra. When "FILE" is selected, the fragmentation methods of spectra are given in the input spectrum data file. Default value: FILE.
-f [ --fixed-mod ] <C57|C58|a fixed modification file>
Set fixed modifications. Three available options: C57, C58, or the name of a text file containing the information of fixed modifications (see an example file). When C57 is selected, carbamidomethylation on cysteine is the only fixed modification. When C58 is selected, carboxymethylation on cysteine is the only fixed modification.
-n [ --n-terminal-form ] <a list of allowed N-terminal forms>
Set N-terminal forms of proteins. Four N-terminal forms can be selected: NONE, NME, NME_ACETYLATION, and M_ACETYLATION. NONE stands for no modifications, NME for N-terminal methionine excision, NME_ACETYLATION for N-terminal acetylation after the initiator methionine is removed, and M_ACETYLATION for N-terminal methionine acetylation. When multiple forms are allowed, they are separated by commas. Default value: NONE,M_ACETYLATION,NME,NME_ACETYLATION.
-d [ --decoy ]
Use a shuffled decoy protein database to estimate spectrum and proteoform level FDRs. When -d is chosen, a shuffled decoy database is automatically generated and appended to the target database before database search, and FDR rates are estimated using the target-decoy approach.
-e [ --mass-error-tolerance ] <a positive integer>
Set the error tolerance for precursor and fragment masses in part-per-million (ppm). Default value: 15. When the lookup table approach (-l) is used for E-value estimation, valid error tolerance values are 5, 10, and 15 ppm.
-p [ --proteoform-error-tolerance ] <a positive number>
Set the error tolerance for identifying PrSM clusters (in Dalton). Default value: 1.2 Dalton.
-M [ --max-shift ] <a number>
Set the maximum value for unexpected mass shifts (in Dalton). Default value: 500.
-m [ --min-shift ] <a number>
Se the minimum value for unexpected mass shifts (in Dalton). Default value: -500.
-s [ --num-shift ] <0|1|2>
Set the maximum number of unexpected mass shifts in a PrSM. Default value: 1.
-t [ --spectrum-cutoff-type ] <EVALUE|FDR>
Set the spectrum level cutoff type for filtering PrSMs. Default value: EVALUE.
-v [ --spectrum-cutoff-value ] <a positive number>
Set the spectrum level cutoff value for filtering PrSMs. Default value: 0.01.
-T [ --proteoform-cutoff-type ] <EVALUE|FDR>
Set the proteoform level cutoff type for filtering proteoforms and PrSMs. Default value: EVALUE.
-V [ --proteoform-cutoff-value ] <a positive number>
Set the proteoform level cutoff value for filtering proteoforms and PrSMs. Default value: 0.01.
-l [ --lookup-table ]
Use a lookup table method for computing p-values and E-values. It is faster than the default generating function approach, but it may reduce the number of identifications.
-r [ --num-combined-spectra ] <a positive integer>
Set the number of combined spectra. The parameter is set to 2 (or 3) for combining spectral pairs (or triplets) generated by the alternating fragmentation mode. Default value: 1.
-i [ --mod-file-name ] <a common modification file>
Specify a text file containing a list of common PTMs for proteoform characterization. The PTMs are used to identify and localize PTMs in reported PrSMs with unknown mass shifts. See an example file.
-H [ --miscore-threshold ] <a number between 0 and 1>
Set the score threshold (MIScore) for filtering results of PTM characterization. Default value: 0.45.
-u [ --thread-number ] <a positive number>
Set the number of threads used in the computation. Default value: 1. The maximum number of threads is determined by the CPU and memory of the computer used for computation. About 4 GB memory is required for each thread. If the computer has 16 GB memory and a CPU with 8 cores, the maximum number of threads is 4 because about 16 GB memory is needed for 4 threads.
-x [ --no-topfd-feature ]
Specify that there are no TopFD feature files for proteoform identification.
-c [ --combined-file-name ] <a filename>
Specify an output file name for combined identifications when the input consists of multiple spectrum files.
-k [ --keep ]
Keep intermediate files generated by TopPIC.