def missed_cleavages(self):
'''Sets the minimum missed cleavages during spectral searching'''
label = widgets.Label("Missed Cleavage Range")
self.layout.addWidget(label, 4, 0, 1, 5)
storage = updating.Storage('minimum_missed_cleavages')
minimum = updating.SpinBox(
self,
storage,
minimum=0,
maximum=5,
tooltip="Minimum number of missed cleavages from "
"proteolytic digestion",
width=50)
self.layout.addWidget(minimum, 4, 8, 1, 1)
storage = updating.Storage('maximum_missed_cleavages')
maximum = updating.SpinBox(
self,
storage,
minimum=0,
maximum=10,
tooltip="Maximum number of missed cleavages from "
"proteolytic digestion",
width=50)
self.layout.addWidget(maximum, 4, 9, 1, 1)
def charge_range(self):
'''Sets the charges to consider above the identified charge'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Charge Range")
hlayout.addWidget(label)
storage = updating.Storage('minus_charge_range')
minus = updating.SpinBox(self, storage,
minimum=0,
maximum=5,
tooltip="Number of charges below the identified charge to "
"include during XIC extraction.",
width=50,
prefix='-')
hlayout.addWidget(minus)
storage = updating.Storage('plus_charge_charge')
plus = updating.SpinBox(self, storage,
minimum=0,
maximum=5,
tooltip="Number of charges above the identified charge to "
"include during XIC extraction.",
width=50,
prefix='+')
hlayout.addWidget(plus)
def peptide_length(self):
'''Sets the minimum peptide length for spectral searching'''
label = widgets.Label("Peptide Length Range")
self.layout.addWidget(label, 3, 0, 1, 5)
storage = updating.Storage('minimum_peptide_length')
minimum = updating.SpinBox(
self,
storage,
minimum=3,
maximum=10,
tooltip="Minimum peptide length included during spectral searches",
width=50)
self.layout.addWidget(minimum, 3, 8, 1, 1)
storage = updating.Storage('maximum_peptide_length')
maximum = updating.SpinBox(
self,
storage,
minimum=20,
maximum=70,
tooltip="Maximum peptide length included during spectral searches",
width=50)
self.layout.addWidget(maximum, 3, 9, 1, 1)
def minimum_crosslinker(self):
'''Sets the maximum modifications fragments per peptide'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Max Modifications")
hlayout.addWidget(label)
storage = updating.Storage('maximum_modifications')
modifications = updating.SpinBox(self, storage,
minimum=0,
maximum=10,
tooltip="Maximum number of modifications per peptide.",
width=75)
hlayout.addWidget(modifications)
def maximum_crosslinkers(self):
'''Sets the maximum crosslinker fragments per peptide'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Max Crosslinkers")
hlayout.addWidget(label)
storage = updating.Storage('maximum_crosslinkers')
crosslinkers = updating.SpinBox(self, storage,
minimum=0,
maximum=10,
tooltip="Maximum number of crosslinker fragments per peptide.",
width=75)
hlayout.addWidget(crosslinkers)
def filtering_range(self):
'''Sets the order of magnitude range for XIC filtering'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Relative Intensity Range")
hlayout.addWidget(label)
storage = updating.Storage('intensity_filtering_range')
range_ = updating.SpinBox(self, storage,
minimum=1,
maximum=10,
preifx="1e",
tooltip="Relative intensity range (set by finding a minimum\n"
"threshold relative to the maximum intensity.",
width=75)
hlayout.addWidget(range_)
def product_level(self):
'''Sets the MS level for the product scan data'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Product")
hlayout.addWidget(label)
storage = updating.Storage('product_scan_level')
level = updating.SpinBox(self,
storage,
minimum=2,
maximum=10,
tooltip="Product Scan Level",
prefix='MS',
width=75)
hlayout.addWidget(level)
def peptide_interval(self):
'''Sets the default peptide interval for the Mowse database'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Peptide Interval")
hlayout.addWidget(label)
storage = updating.Storage('peptide_interval')
interval = updating.SpinBox(
self,
storage,
minimum=1e2,
maximum=1e4,
tooltip="Bin width for grouping peptide in the Mowse database",
width=100,
suffix=' Da')
hlayout.addWidget(interval)
def ppm(self):
'''Sets the maximum PPM error at a given isotope'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("PPM")
hlayout.addWidget(label)
storage = updating.Storage('ppm_threshold')
ppm = updating.SpinBox(
self,
storage,
minimum=0,
maximum=100,
tooltip="Maximum relative error between the experimental and "
"theoretical peptide mass.",
width=75)
hlayout.addWidget(ppm)
def isotopes(self):
'''Sets the number of isotopes to match above monoisotopic'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Isotopes")
hlayout.addWidget(label)
storage = updating.Storage('isotope_threshold')
isotopes = updating.SpinBox(
self,
storage,
minimum=0,
maximum=10,
tooltip="Number of Isotopes above monoisotopic for the intact "
"bridge to be sequenced at.",
width=75)
hlayout.addWidget(isotopes)
def scan_steps(self):
'''Sets the scan steps for precursor scan linking'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Max Steps")
hlayout.addWidget(label)
storage = updating.Storage('precursor_scan_steps')
steps = updating.SpinBox(
self,
storage,
minimum=5,
maximum=1000,
tooltip="Maximum scans preceeding the identified product scan\n"
"to search for the precursor scan.",
width=75)
hlayout.addWidget(steps)
def precursor_intensity(self):
'''Sets the minimum intensity required for precursor matching'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Max Missing Precursors")
hlayout.addWidget(label)
storage = updating.Storage('missing_precursor_threshold')
intensity = updating.SpinBox(
self,
storage,
minimum=0,
maximum=100,
tooltip="Maximum number (percent) of product scans without\n"
"linked precursor scans before reporting mismatched files.",
suffix='%',
width=75)
hlayout.addWidget(intensity)
def mass(self):
'''Sets the low-resolution mass threshold for a link identification'''
hlayout = self.add_layout(QtGui.QHBoxLayout)
label = widgets.Label("Mass")
hlayout.addWidget(label)
storage = updating.Storage('mass_threshold')
mass = updating.SpinBox(
self,
storage,
minimum=0,
maximum=10000,
tooltip="Maximum mass error for a low-resolution "
"identification (low confidence).",
width=100,
suffix=' Da',
singleStep=100)
hlayout.addWidget(mass)