MuCS is a de novo protein sequencing algorithm to assemble full-length protein sequence, it integrates multiple less specific and unspecific hydrolysis strategies (e.g. microwave-assisted acid hydrolysis, papain hydrolysis and proteinase K hydrolysis) to achieve high robustness in the assembly process.

MuCS usage:
1. This version of MuCS should be run in command line and located to the MuCS folder. (cd ../MuCS)
2. De novo peptide sequencing is performed in a separate step. MuCS do not perform de novo peptide sequencing. We recommend to use pNovo or PEAKS to do it. Please download and run either to get the top 10 peptide sequences for each spectra. 
3. The result files are then transformed into fasta format, first line is integrated mass spectra name wth the number of the sequence (i.e. >spec.dta@P1, >spec.dta@P2), second line is the peptide sequence. We provided programs (PEAKS2fasta.exe and pnovocmd2fasta.exe) for this conversion:

****************de novo peptide sequence to fasta format*****************
For PEAKS
PEAKS2fasta.exe -p PEAKS_result.csv -k kmer -o output.fa
Parameter explanation:
-p. The result file from PEAKS
-k. Length of kmer
-o. Output fasta file for MuCS process

For pNovo
pnovocmd2fasta.exe pNovo.res
Parameter explanation:
The input file is the result file from pNovo and the output file is a fasta format file for MuCS process.

4. Run the MuCS main program C-S_assembly.exe to assemble the de novo sequenced peptides into full-length protein sequences.
**************************************run**************************************
C-S_assembly.exe -1 peptide1.fa -2 peptide2.fa -3 peptide3.fa -d denovotype -k kmer -o assembly_prefix -w workfold
Parameter explanation:
-1. De novo peptide sequencing result of hydrolysis strategy 1. fasta format.
-2. De novo peptide sequencing result of hydrolysis strategy 2. fasta format.
-3. De novo peptide sequencing result of hydrolysis strategy 3. fasta format.
-d. De novo sequencing software (PEAKS: 0; pNovo: 1)
-k. Length of kmer (default: 7)
-o. Prefix of assembly result file.
-w. Work and output folder.