Collect parameters for FragPipe-like b-fabric application
b-fabric dataset
-
needs to contain resources generated by timsTOF import application (zip archives of *.d folders)
-
instructs building of philosopher workspace
workspace
|-database
|-parameters
|-<exp>_<rep>
...
philosopher.yaml
Generate using philosopher pipeline --print
in workspace\parameters
match to
commands:
workspace: yes # manage the experiment workspace for the analysis
database: yes # target-decoy database formatting
comet: no # peptide spectrum matching with Comet
msfragger: yes # peptide spectrum matching with MSFragger
peptideprophet: yes # peptide assignment validation
ptmprophet: no # PTM site localization
proteinprophet: yes # protein identification validation
filter: yes # statistical filtering, validation and False Discovery Rates assessment
freequant: no # label-free Quantification
labelquant: no # isobaric Labeling-Based Relative Quantification
bioquant: no # protein report based on Uniprot protein clusters
report: yes # multi-level reporting for both narrow-searches and open-searches
abacus: yes # combined analysis of LC-MS/MS results
tmtintegrator: no # integrates channel abundances from multiple TMT samples
database:
protein_database: /workspace/database/*.fasta # path to the target-decoy protein database
decoy_tag: rev_ # prefix tag used added to decoy sequences
msfragger: # v2.3
path: .../MSFragger-2.3.jar # path to MSFragger jar
memory: 64 # how much memory in GB to use
param: workspace/closed_fragger.params # MSFragger parameter file
raw: d # spectra format
num_threads: 64 # 0=poll CPU to set num threads; else specify num threads directly (max 64)
...
abacus:
protein: true # global level protein report
peptide: false # global level peptide report
proteinProbability: 0.05 # minimum protein probability (default 0.9)
peptideProbability: 0.5 # minimum peptide probability (default 0.5)
uniqueOnly: false # report TMT quantification based on only unique peptides
reprint: yes # create abacus reports using the Reprint format
fragger.params
Generate default parameter files using java -jar MSFragger.jar --config
workspace\parameters
for closed, open, and nonspecific searches. Edit closed_fragger.params according to user selection below.
match to
num_threads = 64 # Number of CPU threads to use.
database_name = /workspace/database/*.fasta # Path to the protein database file in FASTA format.
search_enzyme_name = Trypsin # Name of enzyme to be written to the pepXML file.
search_enzyme_cutafter = KR # Residues after which the enzyme cuts.
search_enzyme_butnotafter = P # Residues that the enzyme will not cut before.
num_enzyme_termini = 2 # 0 for non-enzymatic, 1 for semi-enzymatic, and 2 for fully-enzymatic.
allowed_missed_cleavage = 1 # Allowed number of missed cleavages per peptide. Maximum value is 5.
alternative gluc : cut(DE), nocuts(P) alternative argc : cut(R), nocuts(P)
Be carefull: peptide prophet use trypsin
, gluc
, argc
. see PeptideProphet
IonQuant parameters
Edited by Tobias Kockmann