MSSimulator

Options

version

Version of the tool that generated this parameters file.

log

Name of log file (created only when specified)

debug

Sets the debug level

threads

Sets the number of threads allowed to be used by the TOPP tool

no_progress

Disables progress logging to command line

force

Overrides tool-specific checks

test

Enables the test mode (needed for internal use only)

enzyme

Enzyme to use for digestion (select 'no cleavage' to skip digestion)

model

The cleavage model to use for digestion. 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u).

min_peptide_length

Minimum peptide length after digestion (shorter ones will be discarded)

threshold

Model threshold for calling a cleavage. Higher values increase the number of cleavages. -2 will give no cleavages, +4 almost full cleavage.

missed_cleavages

Maximum number of missed cleavages considered. All possible resulting peptides will be created.

rt_column

Modelling of an RT or CE column

auto_scale

Scale predicted RT's/MT's to given 'total_gradient_time'? If 'true', for CE this means that 'CE:lenght_d', 'CE:length_total', 'CE:voltage' have no influence.

total_gradient_time

The duration [s] of the gradient.

sampling_rate

Time interval [s] between consecutive scans

min

Start of RT Scan Window [s]

max

End of RT Scan Window [s]

feature_stddev

Standard deviation of shift in retention time [s] from predicted model (applied to every single feature independently)

affine_offset

Global offset in retention time [s] from predicted model

affine_scale

Global scaling in retention time from predicted model

distortion

Distortion of the elution profiles. Good presets are 0 for a perfect elution profile, 1 for a slightly distorted elution profile etc... For trapping instruments (e.g. Orbitrap) distortion should be >4.

value

Width of the Exponential Gaussian Hybrid distribution shape of the elution profile. This does not correspond directly to the width in [s].

variance

Random component of the width (set to 0 to disable randomness), i.e. scale parameter for the lorentzian variation of the variance (Note: The scale parameter has to be >= 0).

value

Asymmetric component of the EGH. Higher absolute(!) values lead to more skewness (negative values cause fronting, positive values cause tailing). Tau parameter of the EGH, i.e. time constant of the exponential decay of the Exponential Gaussian Hybrid distribution shape of the elution profile.

variance

Random component of skewness (set to 0 to disable randomness), i.e. scale parameter for the lorentzian variation of the time constant (Note: The scale parameter has to be > 0).

model_file

SVM model for retention time prediction

pH

pH of buffer

alpha

Exponent Alpha used to calculate mobility

mu_eo

Electroosmotic flow

lenght_d

Length of capillary [cm] from injection site to MS

length_total

Total length of capillary [cm]

voltage

Voltage applied to capillary

dt_simulation_on

Modelling detectibility enabled? This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count

min_detect

Minimum peptide detectability accepted. Peptides with a lower score will be removed

dt_model_file

SVM model for peptide detectability prediction

ionized_residues

List of residues (as three letter code) that will be considered during ES ionization. The N-term is always assumed to carry a charge. This parameter will be ignored during MALDI ionization

charge_impurity

List of charged ions that contribute to charge with weight of occurrence (their sum is scaled to 1 internally), e.g. ['H:1'] or ['H:0.7' 'Na:0.3'], ['H:4' 'Na:1'] (which internally translates to ['H:0.8' 'Na:0.2'])

max_impurity_set_size

Maximal #combinations of charge impurities allowed (each generating one feature) per charge state. E.g. assuming charge=3 and this parameter is 2, then we could choose to allow '3H+, 2H+Na+' features (given a certain 'charge_impurity' constraints), but no '3H+, 2H+Na+, 3Na+'

ionization_probability

Probability for the binomial distribution of the ESI charge states

ionization_probabilities

List of probabilities for different charge states (starting at charge=1, 2, ...) during MALDI ionization (the list must sum up to 1.0)

lower_measurement_limit

Lower m/z detector limit

upper_measurement_limit

Upper m/z detector limit

enabled

Enable RAW signal simulation? (select 'false' if you only need feature-maps)

peak_shape

Peak Shape used around each isotope peak (be aware that the area under the curve is constant for both types, but the maximal height will differ (~ 2:3 = Lorentz:Gaussian) due to the wider base of the Lorentzian

value

Instrument resolution at 400 Th

type

How does resolution change with increasing m/z?! QTOFs usually show 'constant' behavior, FTs have linear degradation, and on Orbitraps the resolution decreases with square root of mass

scaling

Scale of baseline. Set to 0 to disable simulation of baseline

shape

The baseline is modeled by an exponential probability density function (pdf) with f(x) = shape*e^(- shape*x)

sampling_points

Number of raw data points per FWHM of the peak

file

Contaminants file with sum formula and absolute RT interval. See 'share/OpenMS/SIMULATION/contaminants.txt' for details

error_mean

Average systematic m/z error (in Da)

error_stddev

Standard deviation for m/z errors. Set to 0 to disable simulation of m/z errors

scale

Constant scale factor of the feature intensity. Set to 1.0 to get the real intensity values provided in the FASTA file

scale_stddev

Standard deviation of peak intensity (relative to the scaled peak height). Set to 0 to get simple rescaled intensities

rate

Poisson rate of shot noise per unit m/z (random peaks in m/z, where the number of peaks per unit m/z follows a Poisson distribution). Set this to 0 to disable simulation of shot noise

intensity-mean

Shot noise intensity mean (exponentially distributed with given mean)

mean

Mean value of white noise (Gaussian) being added to each *measured* signal intensity

stddev

Standard deviation of white noise being added to each *measured* signal intensity

mean

Mean intensity value of the detector noise (Gaussian distribution)

stddev

Standard deviation of the detector noise (Gaussian distribution)

status

Create Tandem-MS scans?

tandem_mode

Algorithm to generate the tandem-MS spectra. 0 - fixed intensities, 1 - SVC prediction (abundant/missing), 2 - SVR prediction of peak intensity

svm_model_set_file

File containing the filenames of SVM Models for different charge variants

ms2_spectra_per_rt_bin

Number of allowed MS/MS spectra in a retention time bin.

min_mz_peak_distance

The minimal distance (in Th) between two peaks for concurrent selection for fragmentation. Also used to define the m/z width of an exclusion window (distance +/- from m/z of precursor). If you set this lower than the isotopic envelope of a peptide, you might get multiple fragment spectra pointing to the same precursor.

mz_isolation_window

All peaks within a mass window (in Th) of a selected peak are also selected for fragmentation.

exclude_overlapping_peaks

If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection.

charge_filter

Charges considered for MS2 fragmentation.

use_dynamic_exclusion

If true dynamic exclusion is applied.

exclusion_time

The time (in seconds) a feature is excluded.

max_list_size

The maximal number of precursors in the inclusion list.

min_rt

Minimal rt in seconds.

max_rt

Maximal rt in seconds.

rt_step_size

rt step size in seconds.

rt_window_size

rt window size in seconds.

min_protein_id_probability

Minimal protein probability for a protein to be considered identified.

min_pt_weight

Minimal pt weight of a precursor

min_mz

Minimal mz to be considered in protein based LP formulation.

max_mz

Minimal mz to be considered in protein based LP formulation.

use_peptide_rule

Use peptide rule instead of minimal protein id probability

min_peptide_ids

If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id

min_peptide_probability

If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified

add_single_spectra

If true, the MS2 spectra for each peptide signal are included in the output (might be a lot). They will have a meta value 'MSE_DebugSpectrum' attached, so they can be filtered out. Native MS_E spectra will have 'MSE_Spectrum' instead.

isotope_model

Model to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks. Note that adding isotopic peaks is very slow.

max_isotope

Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'

max_isotope_probability

Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'

add_metainfo

Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++

add_losses

Adds common losses to those ion expect to have them, only water and ammonia loss is considered

sort_by_position

Sort output by position

add_precursor_peaks

Adds peaks of the unfragmented precursor ion to the spectrum

add_all_precursor_charges

Adds precursor peaks with all charges in the given range

add_abundant_immonium_ions

Add most abundant immonium ions (for Proline, Cystein, Iso/Leucine, Histidin, Phenylalanin, Tyrosine, Tryptophan)

add_first_prefix_ion

If set to true e.g. b1 ions are added

add_y_ions

Add peaks of y-ions to the spectrum

add_b_ions

Add peaks of b-ions to the spectrum

add_a_ions

Add peaks of a-ions to the spectrum

add_c_ions

Add peaks of c-ions to the spectrum

add_x_ions

Add peaks of x-ions to the spectrum

add_z_ions

Add peaks of z-ions to the spectrum

y_intensity

Intensity of the y-ions

b_intensity

Intensity of the b-ions

a_intensity

Intensity of the a-ions

c_intensity

Intensity of the c-ions

x_intensity

Intensity of the x-ions

z_intensity

Intensity of the z-ions

relative_loss_intensity

Intensity of loss ions, in relation to the intact ion intensity

precursor_intensity

Intensity of the precursor peak

precursor_H2O_intensity

Intensity of the H2O loss peak of the precursor

precursor_NH3_intensity

Intensity of the NH3 loss peak of the precursor

add_isotopes

If set to 1 isotope peaks of the product ion peaks are added

max_isotope

Defines the maximal isotopic peak which is added, add_isotopes must be set to 1

add_metainfo

Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++

add_first_prefix_ion

If set to true e.g. b1 ions are added

hide_y_ions

Add peaks of y-ions to the spectrum

hide_y2_ions

Add peaks of y-ions to the spectrum

hide_b_ions

Add peaks of b-ions to the spectrum

hide_b2_ions

Add peaks of b-ions to the spectrum

hide_a_ions

Add peaks of a-ions to the spectrum

hide_c_ions

Add peaks of c-ions to the spectrum

hide_x_ions

Add peaks of x-ions to the spectrum

hide_z_ions

Add peaks of z-ions to the spectrum

hide_losses

Adds common losses to those ion expect to have them, only water and ammonia loss is considered

y_intensity

Intensity of the y-ions

b_intensity

Intensity of the b-ions

a_intensity

Intensity of the a-ions

c_intensity

Intensity of the c-ions

x_intensity

Intensity of the x-ions

z_intensity

Intensity of the z-ions

relative_loss_intensity

Intensity of loss ions, in relation to the intact ion intensity

ionization_type

Type of Ionization (MALDI or ESI)

type

Select the labeling type you want for your experiment

ICPL_fixed_rtshift

Fixed retention time shift between labeled pairs. If set to 0.0 only the retention times, computed by the RT model step are used.

label_proteins

Enables protein-labeling. (select 'false' if you only need peptide-labeling)

ICPL_light_channel_label

UniMod Id of the light channel ICPL label.

ICPL_medium_channel_label

UniMod Id of the medium channel ICPL label.

ICPL_heavy_channel_label

UniMod Id of the heavy channel ICPL label.

fixed_rtshift

Fixed retention time shift between labeled peptides. If set to 0.0 only the retention times computed by the RT model step are used.

modification_lysine

Modification of Lysine in the medium SILAC channel

modification_arginine

Modification of Arginine in the medium SILAC channel

modification_lysine

Modification of Lysine in the heavy SILAC channel. If left empty, two channelSILAC is assumed.

modification_arginine

Modification of Arginine in the heavy SILAC channel. If left empty, two-channel SILAC is assumed.

iTRAQ

4plex or 8plex iTRAQ?

reporter_mass_shift

Allowed shift (uniformly distributed - left to right) in Da from the expected position (of e.g. 114.1, 115.1)

channel_active_4plex

Four-plex only: Each channel that was used in the experiment and its description (114-117) in format <channel>:<name>, e.g. "114:myref","115:liver".

channel_active_8plex

Eight-plex only: Each channel that was used in the experiment and its description (113-121) in format <channel>:<name>, e.g. "113:myref","115:liver","118:lung".

isotope_correction_values_4plex

override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2'

isotope_correction_values_8plex

override default values (see Documentation); use the following format: <channel>:<-2Da>/<-1Da>/<+1Da>/<+2Da> ; e.g. '113:0/0.3/4/0' , '116:0.1/0.3/3/0.2'

Y_contamination

Efficiency of labeling tyrosine ('Y') residues. 0=off, 1=full labeling

labeling_efficiency

Describes the distribution of the labeled peptide over the different states (unlabeled, mono- and di-labeled)

biological

Controls the 'biological' randomness of the generated data (e.g. systematic effects like deviations in RT). If set to 'random' each experiment will look different. If set to 'reproducible' each experiment will have the same outcome (given that the input data is the same)

technical

Controls the 'technical' randomness of the generated data (e.g. noise in the raw signal). If set to 'random' each experiment will look different. If set to 'reproducible' each experiment will have the same outcome (given that the input data is the same)

Views

MSSimulator Std Output

The text sent to standard out during the execution of MSSimulator.

MSSimulator Error Output

The text sent to standard error during the execution of MSSimulator. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

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