diff --git a/docs/source/prediction-models.rst b/docs/source/prediction-models.rst index b0e4eff..c8a41db 100644 --- a/docs/source/prediction-models.rst +++ b/docs/source/prediction-models.rst @@ -88,287 +88,287 @@ The table below lists and describes all features generated and used by MS²PIP. based on four amino acid properties (basicity, hydrophobicity, helicity and isoelectric point) for the full precursor and for the N- and C-terminal ions. -+-----------------+--------------------------------------------------------------+ -| Feature | Description | -+=================+==============================================================+ -| ``p_length`` | Precursor length | -+-----------------+--------------------------------------------------------------+ -| ``p_charge`` | Precursor charge | -+-----------------+--------------------------------------------------------------+ -| ``p_charge1`` | Precursor charge is 1 (one-hot encoding) | -+-----------------+--------------------------------------------------------------+ -| ``p_charge2`` | Precursor charge is 2 (one-hot encoding) | -+-----------------+--------------------------------------------------------------+ -| ``p_charge3`` | Precursor charge is 3 (one-hot encoding) | -+-----------------+--------------------------------------------------------------+ -| ``p_charge4`` | Precursor charge is 4 (one-hot encoding) | -+-----------------+--------------------------------------------------------------+ -| ``p_charge5`` | Precursor charge is 5 (one-hot encoding) | -+-----------------+--------------------------------------------------------------+ -| ``p_basi_min`` | Minimum basicity of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_basi_q1`` | First quartile of basicity of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_basi_q2`` | Second quartile of basicity of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_basi_q3`` | Third quartile of basicity of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_basi_max`` | Maximum basicity of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_heli_min`` | Minimum helicity of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_heli_q1`` | First quartile of helicity of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_heli_q2`` | Second quartile of helicity of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_heli_q3`` | Third quartile of helicity of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_heli_max`` | Maximum helicity of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_hydro_min`` | Minimum hydrophobicity of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_hydro_q1`` | First quartile of hydrophobicity of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_hydro_q2`` | Second quartile of hydrophobicity of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_hydro_q3`` | Third quartile of hydrophobicity of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_hydro_max`` | Maximum hydrophobicity of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_iso_min`` | Minimum isoelectric point of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_iso_q1`` | First quartile of isoelectric point of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_iso_q2`` | Second quartile of isoelectric point of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_iso_q3`` | Third quartile of isoelectric point of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p_iso_max`` | Maximum isoelectric point of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``n_length`` | Length of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_length`` | Length of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_A`` | Count of amino acid 'A' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_A`` | Count of amino acid 'A' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_C`` | Count of amino acid 'C' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_C`` | Count of amino acid 'C' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_D`` | Count of amino acid 'D' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_D`` | Count of amino acid 'D' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_E`` | Count of amino acid 'E' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_E`` | Count of amino acid 'E' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_F`` | Count of amino acid 'F' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_F`` | Count of amino acid 'F' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_G`` | Count of amino acid 'G' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_G`` | Count of amino acid 'G' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_H`` | Count of amino acid 'H' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_H`` | Count of amino acid 'H' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_I`` | Count of amino acid 'I' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_I`` | Count of amino acid 'I' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_K`` | Count of amino acid 'K' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_K`` | Count of amino acid 'K' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_M`` | Count of amino acid 'M' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_M`` | Count of amino acid 'M' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_N`` | Count of amino acid 'N' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_N`` | Count of amino acid 'N' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_P`` | Count of amino acid 'P' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_P`` | Count of amino acid 'P' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_Q`` | Count of amino acid 'Q' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_Q`` | Count of amino acid 'Q' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_R`` | Count of amino acid 'R' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_R`` | Count of amino acid 'R' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_S`` | Count of amino acid 'S' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_S`` | Count of amino acid 'S' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_T`` | Count of amino acid 'T' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_T`` | Count of amino acid 'T' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_V`` | Count of amino acid 'V' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_V`` | Count of amino acid 'V' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_W`` | Count of amino acid 'W' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_W`` | Count of amino acid 'W' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_count_Y`` | Count of amino acid 'Y' in the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_count_Y`` | Count of amino acid 'Y' in the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``p0_basi`` | Basicity of the 0th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p-1_basi`` | Basicity of the -1th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``pi-1_basi`` | Basicity of the (i-1)th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``pi_basi`` | Basicity of the ith position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``pi+1_basi`` | Basicity of the (i+1)th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``pi+2_basi`` | Basicity of the (i+2)th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``n_basi_sum`` | Sum of basicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_basi_min`` | Minimum basicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_basi_q1`` | First quartile of basicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_basi_q2`` | Second quartile of basicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_basi_q3`` | Third quartile of basicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_basi_max`` | Maximum basicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_basi_sum`` | Sum of basicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_basi_min`` | Minimum basicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_basi_q1`` | First quartile of basicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_basi_q2`` | Second quartile of basicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_basi_q3`` | Third quartile of basicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_basi_max`` | Maximum basicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``p0_heli`` | Helicity of the 0th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p-1_heli`` | Helicity of the -1th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``pi-1_heli`` | Helicity of the (i-1)th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``pi_heli`` | Helicity of the ith position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``pi+1_heli`` | Helicity of the (i+1)th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``pi+2_heli`` | Helicity of the (i+2)th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``n_heli_sum`` | Sum of helicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_heli_min`` | Minimum helicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_heli_q1`` | First quartile of helicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_heli_q2`` | Second quartile of helicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_heli_q3`` | Third quartile of helicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_heli_max`` | Maximum helicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_heli_sum`` | Sum of helicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_heli_min`` | Minimum helicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_heli_q1`` | First quartile of helicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_heli_q2`` | Second quartile of helicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_heli_q3`` | Third quartile of helicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_heli_max`` | Maximum helicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``p0_hydro`` | Hydrophobicity of the 0th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p-1_hydro`` | Hydrophobicity of the -1th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``pi-1_hydro`` | Hydrophobicity of the (i-1)th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``pi_hydro`` | Hydrophobicity of the ith position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``pi+1_hydro`` | Hydrophobicity of the (i+1)th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``pi+2_hydro`` | Hydrophobicity of the (i+2)th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``n_hydro_sum`` | Sum of hydrophobicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_hydro_min`` | Minimum hydrophobicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_hydro_q1`` | First quartile of hydrophobicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_hydro_q2`` | Second quartile of hydrophobicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_hydro_q3`` | Third quartile of hydrophobicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_hydro_max`` | Maximum hydrophobicity of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_hydro_sum`` | Sum of hydrophobicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_hydro_min`` | Minimum hydrophobicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_hydro_q1`` | First quartile of hydrophobicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_hydro_q2`` | Second quartile of hydrophobicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_hydro_q3`` | Third quartile of hydrophobicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_hydro_max`` | Maximum hydrophobicity of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``p0_iso`` | Isoelectric point of the 0th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``p-1_iso`` | Isoelectric point of the -1th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``pi-1_iso`` | Isoelectric point of the (i-1)th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``pi_iso`` | Isoelectric point of the ith position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``pi+1_iso`` | Isoelectric point of the (i+1)th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``pi+2_iso`` | Isoelectric point of the (i+2)th position of the precursor | -+-----------------+--------------------------------------------------------------+ -| ``n_iso_sum`` | Sum of isoelectric points of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_iso_min`` | Minimum isoelectric point of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_iso_q1`` | First quartile of isoelectric points of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_iso_q2`` | Second quartile of isoelectric points of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_iso_q3`` | Third quartile of isoelectric points of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``n_iso_max`` | Maximum isoelectric point of the N-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_iso_sum`` | Sum of isoelectric points of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_iso_min`` | Minimum isoelectric point of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_iso_q1`` | First quartile of isoelectric points of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_iso_q2`` | Second quartile of isoelectric points of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_iso_q3`` | Third quartile of isoelectric points of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ -| ``c_iso_max`` | Maximum isoelectric point of the C-terminal ion | -+-----------------+--------------------------------------------------------------+ ++-----------------+----------------------------------------------------------------------+ +| Feature | Description | ++=================+======================================================================+ +| ``p_length`` | Precursor length | ++-----------------+----------------------------------------------------------------------+ +| ``p_charge`` | Precursor charge | ++-----------------+----------------------------------------------------------------------+ +| ``p_charge1`` | Precursor charge is 1 (one-hot encoding) | ++-----------------+----------------------------------------------------------------------+ +| ``p_charge2`` | Precursor charge is 2 (one-hot encoding) | ++-----------------+----------------------------------------------------------------------+ +| ``p_charge3`` | Precursor charge is 3 (one-hot encoding) | ++-----------------+----------------------------------------------------------------------+ +| ``p_charge4`` | Precursor charge is 4 (one-hot encoding) | ++-----------------+----------------------------------------------------------------------+ +| ``p_charge5`` | Precursor charge is 5 (one-hot encoding) | ++-----------------+----------------------------------------------------------------------+ +| ``p_basi_min`` | Minimum basicity of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_basi_q1`` | First quartile of basicity of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_basi_q2`` | Second quartile of basicity of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_basi_q3`` | Third quartile of basicity of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_basi_max`` | Maximum basicity of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_heli_min`` | Minimum helicity of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_heli_q1`` | First quartile of helicity of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_heli_q2`` | Second quartile of helicity of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_heli_q3`` | Third quartile of helicity of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_heli_max`` | Maximum helicity of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_hydro_min`` | Minimum hydrophobicity of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_hydro_q1`` | First quartile of hydrophobicity of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_hydro_q2`` | Second quartile of hydrophobicity of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_hydro_q3`` | Third quartile of hydrophobicity of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_hydro_max`` | Maximum hydrophobicity of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_iso_min`` | Minimum isoelectric point of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_iso_q1`` | First quartile of isoelectric point of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_iso_q2`` | Second quartile of isoelectric point of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_iso_q3`` | Third quartile of isoelectric point of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``p_iso_max`` | Maximum isoelectric point of the precursor | ++-----------------+----------------------------------------------------------------------+ +| ``n_length`` | Length of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_length`` | Length of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_A`` | Count of amino acid 'A' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_A`` | Count of amino acid 'A' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_C`` | Count of amino acid 'C' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_C`` | Count of amino acid 'C' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_D`` | Count of amino acid 'D' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_D`` | Count of amino acid 'D' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_E`` | Count of amino acid 'E' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_E`` | Count of amino acid 'E' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_F`` | Count of amino acid 'F' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_F`` | Count of amino acid 'F' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_G`` | Count of amino acid 'G' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_G`` | Count of amino acid 'G' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_H`` | Count of amino acid 'H' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_H`` | Count of amino acid 'H' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_I`` | Count of amino acid 'I' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_I`` | Count of amino acid 'I' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_K`` | Count of amino acid 'K' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_K`` | Count of amino acid 'K' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_M`` | Count of amino acid 'M' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_M`` | Count of amino acid 'M' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_N`` | Count of amino acid 'N' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_N`` | Count of amino acid 'N' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_P`` | Count of amino acid 'P' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_P`` | Count of amino acid 'P' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_Q`` | Count of amino acid 'Q' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_Q`` | Count of amino acid 'Q' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_R`` | Count of amino acid 'R' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_R`` | Count of amino acid 'R' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_S`` | Count of amino acid 'S' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_S`` | Count of amino acid 'S' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_T`` | Count of amino acid 'T' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_T`` | Count of amino acid 'T' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_V`` | Count of amino acid 'V' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_V`` | Count of amino acid 'V' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_W`` | Count of amino acid 'W' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_W`` | Count of amino acid 'W' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_count_Y`` | Count of amino acid 'Y' in the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_count_Y`` | Count of amino acid 'Y' in the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``p0_basi`` | basicity of the first amino acid of the peptide | ++-----------------+----------------------------------------------------------------------+ +| ``p-1_basi`` | basicity of the last amino acid of the peptide | ++-----------------+----------------------------------------------------------------------+ +| ``pi-1_basi`` | basicity of the amino acid before the fragmentation site | ++-----------------+----------------------------------------------------------------------+ +| ``pi_basi`` | basicity of the amino acid at the fragmentation site | ++-----------------+----------------------------------------------------------------------+ +| ``pi+1_basi`` | basicity of the 1st amino acid after the fragmentation site | ++-----------------+----------------------------------------------------------------------+ +| ``pi+2_basi`` | basicity of the 2nd amino acid after the fragmentation site | ++-----------------+----------------------------------------------------------------------+ +| ``n_basi_sum`` | Sum of basicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_basi_min`` | Minimum basicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_basi_q1`` | First quartile of basicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_basi_q2`` | Second quartile of basicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_basi_q3`` | Third quartile of basicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_basi_max`` | Maximum basicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_basi_sum`` | Sum of basicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_basi_min`` | Minimum basicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_basi_q1`` | First quartile of basicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_basi_q2`` | Second quartile of basicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_basi_q3`` | Third quartile of basicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_basi_max`` | Maximum basicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``p0_heli`` | Helicity of the first amino acid of the peptide | ++-----------------+----------------------------------------------------------------------+ +| ``p-1_heli`` | Helicity of the last amino acid of the peptide | ++-----------------+----------------------------------------------------------------------+ +| ``pi-1_heli`` | Helicity of the amino acid before the fragmentation site | ++-----------------+----------------------------------------------------------------------+ +| ``pi_heli`` | Helicity of the amino acid at the fragmentation site | ++-----------------+----------------------------------------------------------------------+ +| ``pi+1_heli`` | Helicity of the 1st amino acid after the fragmentation site | ++-----------------+----------------------------------------------------------------------+ +| ``pi+2_heli`` | Helicity of the 2nd amino acid after the fragmentation site | ++-----------------+----------------------------------------------------------------------+ +| ``n_heli_sum`` | Sum of helicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_heli_min`` | Minimum helicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_heli_q1`` | First quartile of helicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_heli_q2`` | Second quartile of helicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_heli_q3`` | Third quartile of helicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_heli_max`` | Maximum helicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_heli_sum`` | Sum of helicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_heli_min`` | Minimum helicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_heli_q1`` | First quartile of helicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_heli_q2`` | Second quartile of helicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_heli_q3`` | Third quartile of helicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_heli_max`` | Maximum helicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``p0_hydro`` | Hydrophobicity of the first amino acid of the peptide | ++-----------------+----------------------------------------------------------------------+ +| ``p-1_hydro`` | Hydrophobicity of the last amino acid of the peptide | ++-----------------+----------------------------------------------------------------------+ +| ``pi-1_hydro`` | Hydrophobicity of the amino acid before the fragmentation site | ++-----------------+----------------------------------------------------------------------+ +| ``pi_hydro`` | Hydrophobicity of the amino acid at the fragmentation site | ++-----------------+----------------------------------------------------------------------+ +| ``pi+1_hydro`` | Hydrophobicity of the 1st amino acid after the fragmentation site | ++-----------------+----------------------------------------------------------------------+ +| ``pi+2_hydro`` | Hydrophobicity of the 2nd amino acid after the fragmentation site | ++-----------------+----------------------------------------------------------------------+ +| ``n_hydro_sum`` | Sum of hydrophobicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_hydro_min`` | Minimum hydrophobicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_hydro_q1`` | First quartile of hydrophobicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_hydro_q2`` | Second quartile of hydrophobicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_hydro_q3`` | Third quartile of hydrophobicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_hydro_max`` | Maximum hydrophobicity of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_hydro_sum`` | Sum of hydrophobicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_hydro_min`` | Minimum hydrophobicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_hydro_q1`` | First quartile of hydrophobicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_hydro_q2`` | Second quartile of hydrophobicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_hydro_q3`` | Third quartile of hydrophobicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_hydro_max`` | Maximum hydrophobicity of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``p0_iso`` | Isoelectric point of the first amino acid of the peptide | ++-----------------+----------------------------------------------------------------------+ +| ``p-1_iso`` | Isoelectric point of the last amino acid of the peptide | ++-----------------+----------------------------------------------------------------------+ +| ``pi-1_iso`` | Isoelectric point of the amino acid before the fragmentation site | ++-----------------+----------------------------------------------------------------------+ +| ``pi_iso`` | Isoelectric point of the amino acid at the fragmentation site | ++-----------------+----------------------------------------------------------------------+ +| ``pi+1_iso`` | Isoelectric point of the 1st amino acid after the fragmentation site | ++-----------------+----------------------------------------------------------------------+ +| ``pi+2_iso`` | Isoelectric point of the 2nd amino acid after the fragmentation site | ++-----------------+----------------------------------------------------------------------+ +| ``n_iso_sum`` | Sum of isoelectric points of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_iso_min`` | Minimum isoelectric point of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_iso_q1`` | First quartile of isoelectric points of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_iso_q2`` | Second quartile of isoelectric points of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_iso_q3`` | Third quartile of isoelectric points of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``n_iso_max`` | Maximum isoelectric point of the N-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_iso_sum`` | Sum of isoelectric points of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_iso_min`` | Minimum isoelectric point of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_iso_q1`` | First quartile of isoelectric points of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_iso_q2`` | Second quartile of isoelectric points of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_iso_q3`` | Third quartile of isoelectric points of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ +| ``c_iso_max`` | Maximum isoelectric point of the C-terminal ion | ++-----------------+----------------------------------------------------------------------+ .. _MassIVE-KB: https://doi.org/10.1016/j.cels.2018.08.004