-a <algorithm> |
Chooses the algorithm for analyzing combinations of multiple
peptide/protein isotope distributions. There are five algorithms to choose from:
Basic - Computes all combinatorial possibilities and returns the
combination with the highest score.
FewestPeptides - Computes increasing depths of combinations until
the score threshold is exceeded. The smallest combination exceeding the threshold
is returned, preventing "over-fitting" of the data.
FastFewestPeptides - Same as the FewestPeptides algorithm, but
trades memory usage for speed. Use this method if there is sufficient memory on the
system.
FewestPeptidesChoice - Same as the FewestPeptides algorithm,
but adds a heuristic to evaluate if further combinatorial analysis would produce a
better score. This method can dramatically improve speed, but may not be as accurate.
FastFewestPeptidesChoice - Same as the FewestPeptidesChoice
algorithm, but trades memory usage for speed. Use this method if there is sufficient
memory on the system.
The default setting is Basic.
|
-cdm <char> |
Chooses the charge state determination method. There are five methods to choose from:
B - Basic method, assume all charge states are possible.
F - Fast Fourier Transform.
P - Patterson algorithm.
Q - QuickCharge method, uses inverse peak distances.
S - Senko method, or combined Fast Fourier Transform and Patterson algorithm.
The default setting is B.
|
-chMin <int> |
Sets the minimum charge state to look for when analyzing a spectrum. The
default value is 1.
|
-chMax <int> |
Sets the maximum charge state to look for when analyzing a spectrum. The
default value is 3.
|
-corr <float> |
Sets the correlation threshold to accept a predicted isotope distribution.
Valid values are any decimal value between 0.0 and 1.0, inclusive. The default
value is 0.90.
|
-d <int> |
Sets the depth of combinatorial analysis. This is the maximum number of
protein/peptide distributions that can be combined to estimate the observed
data at any given spectrum segment. The default value is 3.
|
-hdat <Hardklör DAT file> |
Gives the full path and file name of the Hardklör data file (typically Hardklor.dat) to be used in the
analysis. This flag must be set globally at the top of a config file if the data file
to be used is not in the working directory.
|
-i |
Sets peak detection to intersection mode. Spectra are analyzed for peaks in
overlapping segments. When intersection mode is set, peaks are only accepted if
they appear in two overlapping segments. Intersection is turned on by default.
|
-m <modification> |
Includes alternative averagine models in the analysis that incorporate
additional atoms and/or isotopic enrichments. Modifications are represented as
text strings. Inclusion of additional atoms in the model is done using by
entering an atomic formula,such as: PO2 or Cl.
Inclusion of isotopic enrichment to the model is done by specifying the percent
enrichment (as a decimal) followed by the atom being enriched and an index of
the isotope. For example, 0.75H1 specifies 75% enrichment of the
first heavy isotope of hydrogen. In other words, 75% deuterium enrichment. Two
or more modifications can be combined into the same model, and separated by
spaces: B2 0.5B1
This parameter can also be used redundantly to include multiple alternative
averagine models in a single analysis.
|
-mdat <Mercury DAT file> |
Gives the full path and file name of the Mercury data file (typically ISOTOPE.DAT) to be used in the
analysis. This flag must be set globally at the top of a config file if the data file
to be used is not in the working directory.
|
-mF <Filter Code> |
Sets a filter for mzXML files. If you want to analyze only the MS2 scans in your
mzXML file, specify -mF MS2. Valid values are MS1, MS2, MS3.
|
-nb |
Specifies "no base" averagine. Only modified averagine models will be used
in the analysis.
|
-p <int> |
Sets the maximum number of peptides or proteins that are estimated from the peaks
found in a spectrum segment. The default value is 10.
|
-res <double> <MS> |
Sets the resolution of the observed spectra at m/z 400. The user must specify a
resolution followed by a mass spectrometer code. Valid codes are FTICR,
OrbiTrap, TOF, and QIT. The default settings
are 100000 FTICR.
|
-s <int> |
Applies polynomial Savitsky-Golay smoothing of the mass spectra prior to analysis.
The integer supplied with the flag sets the width of the smoothing window. A larger
width makes smoother peaks, but has more alteration of peak intensity. By default
there is no smoothing.
|
-sc <int> <int> |
Performs analysis on a specific spectrum or set of spectra in the input file.
The user specifies the specta by scan number. The user may specify a single
spectrum, ex: -s 523, or a range of spectra, ex: -s 300 500.
|
-sl <int> |
Sets the sensitivity level. There are four levels, 0 (low), 1 (moderate), 2 (high),
and 3 (max). Increasing the sensitivity may increase computation time. The default value
is 1. |
-sn <float> |
Sets the signal-over-noise threshold. Any integer or decimal value greater
than or equal to 0.0 is valid. The default value is 3.0. |
-snWin <float> |
Sets the signal-over-noise window length (in m/z). Because noise may be non-uniform
across a spectra, this value adjusts the segment size considered when calculating
a signal-over-noise ratio. The default value is 50.0. |
-u |
Sets peak detection to union mode. Spectra are analyzed for peaks in
overlapping segments. When union mode is set, peaks are accepted regardless of
whether they appear in one segment or two overlapping segments. Union is turned
off by default.
|
-w <double> <double> |
Narrows analysis to only a small window in each segment (in m/z). The user must specify
the starting and ending m/z values between which the analysis will be performed. By
default the whole spectrum is analyzed.
|
-win <float> |
Sets the maximum width of any set of peaks in a spectrum when computing the results (in m/z).
Thus, if the value was 5.0, then sets of peaks greater than 5 m/z are divided into
smaller sets prior to analysis. The default value is 5.0. |
