This is the library creation module of a much larger project. The basic idea is to generate peptides from artificially digested proteins.

Simply type 'Make' and then 'make run' to run the supplied fasta file, test.fasta. Make generates an executable called 'main'. To digest other fasta files simply type: ./main test.fasta

The premise of the program is simple, given a protein:

LLHSLKIHNNTASQKTALMEQYDRYLIVENLYYRGLVSQDINIMQNVFYKELLAHVDTIP

If cleaved at all K's and R's (trypsin), this protein would generate fragments like this: 691.438 LLHSLK 993.499 IHNNTASQK 1107.5 TALMEQYDR 1326.7 YLIVENLYYR 1684.94 LLHSLKIHNNTASQK 1849.94 GLVSQDINIMQNVFYK 2101 IHNNTASQKTALMEQYDR 2434.2 TALMEQYDRYLIVENLYYR 3176.64 YLIVENLYYRGLVSQDINIMQNVFYK

Where the first column correspond to the neutral mass of the fragments. Amino acid masses are defined in AminoAcidMasses.h.

It is also possible that trypsin might not digest everything perfectly. There are two types of imperfect digestion, missed cleaveage and semi-tryptic. A missed cleaveage would correspond to a simple concatenation of two adjacent fully tryptic peptides:

LLHSLK + IHNNTASQK = LLHSLKIHNNTASQK

Semi-tryptic means that only one end of the peptide has a tryptic termini, all semi tryptic peptides of GLVSQDINIMQNVFYK: G LVSQDINIMQNVFYK GL VSQDINIMQNVFYK GLV SQDINIMQNVFYK GLVS QDINIMQNVFYK GLVSQ DINIMQNVFYK GLVSQD INIMQNVFYK GLVSQDI NIMQNVFYK GLVSQDIN IMQNVFYK GLVSQDINI MQNVFYK GLVSQDINIM QNVFYK GLVSQDINIMQ NVFYK GLVSQDINIMQN VFYK GLVSQDINIMQNV FYK GLVSQDINIMQNVF YK GLVSQDINIMQNVFY K