Secuenciación de novo. Prácticas. Salvador Martínez de Bartolomé Bioinformatics Support ProteoRed firstname.lastname@example.org. Why de novo sequencing is difficult. Leucine and isoleucine have the same mass Glutamine and lysine differ in mass by 0.036Da
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Salvador Martínez de Bartolomé
Bioinformatics Support ProteoRed
Los problemas asociados a los algoritmos globales eran principalmente dos:
Sherenga (included in SpectrumMill)*
(in “C:\Documents and Settings\Bioworks32\Desktop\denovo\LUTEFISK” folder)
>PepNovo.exe –list paths_of_lots_of_spectra.txt –model CID_IT_TRYP –PTMs C+57:M+16 –digest TRYPSIN
This command runs Pepnovo on all the spectra files in “paths_of_lots_of_spectra.txt” assumes that peptides were digested with trypsin and that the cystine are carbomethylated and that the methionine can be oxidized. The output is the defaults output of 20 sequences.
>PepNovo.exe –file my_great_spectra.mgf –model CID_IT_TRYP C+57:M+16 –digest NON_SPECIFIC –tag_length 3 –num_solutions 50
Runs pepnovo on a single mgf file and generates 50 tags of length 3 for each spectrum (assumes that the digest was not with trypsin).
(in “C:\Documents and Settings\Bioworks32\Desktop\denovo\pepNovo” folder)
PepNovo.exe –file 241103plata_bernabe.369.369.2.dta –model CID_IT_TRYP –digest TRYPSIN
PepNovo.exe –file FQSEEQQQTEDELQDK.dta –model CID_IT_TRYP –digest TRYPSIN