# Parameters¶

pyQms default params, parsed from current params.py file.

Note

This sphinx source file was auto-generated using pyqms/docs/parse_params_for_docu.py, which parses pyqms/params.py Please do not modify this file directly, but rather the original parameter files!



>>> params = {
'BUILD_RESULT_INDEX'' : True,
'COLORS'' : {0.0: (37, 37, 37), 0.1: (99, 99, 99), 0.2: (150, 150, 150), 0.3: (204, 204, 204), 0.4: (247, 247, 247), 0.5: (203, 27, 29), 0.6: (248, 120, 72), 0.7: (253, 219, 121), 0.8: (209, 239, 121), 0.9: (129, 202, 78), 1: (27, 137, 62)},
'ELEMENT_MIN_ABUNDANCE'' : 0.001,
'FIXED_LABEL_ISOTOPE_ENRICHMENT_LEVELS'' : {'15N': 0.994, '13C': 0.996, '2H': 0.994},
'INTENSITY_TRANSFORMATION_FACTOR'' : 100000.0,
'INTERNAL_PRECISION'' : 1000,
'LOWER_MZ_LIMIT'' : 150,
'MACHINE_OFFSET_IN_PPM'' : 0.0,
'MAX_MOLECULES_PER_MATCH_BIN'' : 20,
'MINIMUM_NUMBER_OF_MATCHED_ISOTOPOLOGUES'' : 2,
'MIN_REL_PEAK_INTENSITY_FOR_MATCHING'' : 0.01,
'MZ_SCORE_PERCENTILE'' : 0.4,
'MZ_TRANSFORMATION_FACTOR'' : 10000,
'M_SCORE_THRESHOLD'' : 0.5,
'PERCENTILE_FORMAT_STRING'' : {0:.3f},
'REL_I_RANGE'' : 0.2,
'REL_MZ_RANGE'' : 5e-06,
'REQUIRED_PERCENTILE_PEAK_OVERLAP'' : 0.5,
'SILAC_AAS_LOCKED_IN_EXPERIMENT'' : None,
'UPPER_MZ_LIMIT'' : 2000,
}


## Descriptions¶

### REQUIRED_PERCENTILE_PEAK_OVERLAP¶

Defines the percentile how many theoretical and measured peaks must overlap so that the match is considered further. E.g. 0.5 dictates, that 2 of 4 peaks must ovelap

Default value: 0.5

### ELEMENT_MIN_ABUNDANCE¶

Defines the minimum abundance of an element to be considered for the calculation of the isotopologue(s)

Default value: 0.001

### MIN_REL_PEAK_INTENSITY_FOR_MATCHING¶

Defines the relative minimum peak intensity within an isotopologue to be considered for matching

Default value: 0.01

### REL_I_RANGE¶

Defines the relative intensity error range. Represents the relative error to the most intense peak.

Default value: 0.2

### REL_MZ_RANGE¶

Defines the relative m/z error range or the measuring precision of the used mass spectrometer. Is equal to the precision of the used machine in parts per million (ppm)

Default value: 5e-06

### MZ_SCORE_PERCENTILE¶

Defines the weighting between the m/z error and the intensity error for the total score. This weighting can be adjusted for different mass spectrometers, depending on whether m/z or intensity can be measured more accurately

Default value: 0.4

### MINIMUM_NUMBER_OF_MATCHED_ISOTOPOLOGUES¶

Number of isotopologue peaks that are required to yield a mScore. Very small molecules may yield only one isotope peak (monoisotopic peak) or the non-monoisotopic peaks have a very low abundance, so that they ware not considered for macthing

Default value: 2

### UPPER_MZ_LIMIT¶

Defines the maximum m/z value to be considered by pyQms. Can be adjusted for better performance of pyQms or to limit for the measuring range of the used mass spectrometer

Default value: 2000

### LOWER_MZ_LIMIT¶

Defines the minimum m/z value to be considered by pyQms. Can be adjusted for better performance of pyQms or to limit for the measuring range of the used mass spectrometer

Default value: 150

### MACHINE_OFFSET_IN_PPM¶

A mass spectrometer measuring error (constant machine/calibration dependent mass or m/z offset) can be defined here in parts per million (ppm)

Default value: 0.0

### M_SCORE_THRESHOLD¶

The minimum mScore, which should be reported. Typically a mScore above 0.7 yields a FDR below 1%. Lower mScore thresholds can be used to check for machine errors or to optimize matching of pulse-chase samples

Default value: 0.5

### SILAC_AAS_LOCKED_IN_EXPERIMENT¶

These aminoacids have always the defined fixed SILCA modification and their atoms are not considered when calculating a partially labeling percentile

Default value: None

### PERCENTILE_FORMAT_STRING¶

Defines the standard format string when formatting labeling percentile float. Standard format considers three floating points

Default value: {0:.3f}

### INTERNAL_PRECISION¶

Defines the internal precision for float to int conversion

Default value: 1000

### MAX_MOLECULES_PER_MATCH_BIN¶

Defines the number of molecules per match bin. Influences the matching speed

Default value: 20

### MZ_TRANSFORMATION_FACTOR¶

All m/z values are transformed by this factor This value will be multiplied with m/z values before converted to integer. This means that values with a difference of 0.1 ppm @ 1000 m/z won’t be distinguishable

Default value: 10000

### INTENSITY_TRANSFORMATION_FACTOR¶

All intensities are transformed with this factor

Default value: 100000.0

### BUILD_RESULT_INDEX¶

The results are indexed for faster access

Default value: True