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Detect variants from mass spectra data
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quilts-WU/v1.0
MSGFDB_CompRef_Phospho_iTRAQ_20ppm.txt
MSGFDB_CompRef_iTRAQ_20ppm.txt
PepScan.pl
README.md
db_snpindel.pl
get_confirmed_snps_v1.pl
peptide_table_msgf.pl
protein_seq_for_indel_using_bed.pl
proteome.bed

README.md

PepScan

Detecting peptides from mass spectra data

Song Cao

Usage: perl PepScan.pl run_dir_in run_dir_out step_number

[1] Run Quilts for the annotation of snvs and in-house script for the annotation of indels

[2] Create fasta DB for MSGF+

[3] Run MSGF+ for one sample

[4] Run MSGF+ for multiple samples

[5] Convert mzid to tsv file

[6] Get the number of SAAVs, independent on mass type

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