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Created at Unimelb
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Create
Create a new mzML file set
Required
Configure peptide inputs
Select Input Type
MaxQuant
Prosit
MaxQuant evidence.txt file:
MaxQuant msms.txt file:
MaxQuant PEP threshold:
Filter Terms:
Prosit library file:
Prosit peptide abundance mean:
Prosit peptide abundance stdev:
Prosit peptide abundance emg k:
Prosit peptide abundance model:
gaussian
exponentially_modified_gaussian
cauchy
Optional
Configure DIA acquisition schema
Acquisition schema file:
Optional
Configure mass spectrometry parameters
MS1 min mz:
MS1 max mz:
MS2 min mz:
MS2 max mz:
MS1 resolution:
MS2 resolution:
MS1 scan duration:
MS2 scan duration:
Isolation window:
Spray instability:
Resolution at:
MS1 ppm error mean:
MS1 ppm error stdev:
MS2 ppm error mean:
MS2 ppm error stdev:
Centroid ms1:
Centroid ms2:
Optional
Configure chromatography parameters
Rt peak fwhm distribution model:
gaussian
exponentially_modified_gaussian
cauchy
Rt peak fwhm distribution mean:
Rt peak fwhm distribution stdev:
Rt peak fwhm distribution emg k:
Min rt peak fwhm:
Original run length:
New run length:
RT buffer:
RT instability:
Optional
Configure decoy ions
Decoy .MSP file:
Number of decoys to simulate:
Simulate top n decoy fragments:
Decoy abundance mean:
Decoy abundance stdev:
Optional
Configure quantitation and grouping
N groups:
Samples per group:
Between group standard deviation:
Within group standard deviation:
Probability missing in sample:
Probability missing in group:
Optional
Configure plots
TIC:
Schema:
All:
Optional
Configure advanced parameters
N points greater than fwhm:
MS1 min peak intensity:
MS2 min peak intensity:
Write empty spectra:
Mass spectral peak model:
gaussian
exponentially_modified_gaussian
cauchy
Chromatographic peak model:
gaussian
exponentially_modified_gaussian
cauchy
m/z emg k:
chromatographic emg k:
No isotopes: