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Modified the code to accommodate terminal unmodified amino acids following patterns eg. K$ #1

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Modified the code to accommodate terminal unmodified amino acids following patterns eg. K$ #1

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17a6c17
Very first README
Nov 1, 2017
99ad702
Simple implementation to handle terminal unmodified Lysine while othe…
Nov 9, 2017
2093b2b
Merge remote-tracking branch 'origin/master'
anilkmg Nov 9, 2017
b25b010
Implemented regex comparison to handle terminal unmodified amino acid…
anilkmg Nov 15, 2017
9569d21
Implemented regex comparison to handle terminal unmodified amino acid…
anilkmg Nov 16, 2017
8ecedb5
Nothing but removed the semicolons from lines with debug print statem…
anilkmg Nov 16, 2017
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3 changes: 3 additions & 0 deletions README
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
This project is a forked version of pyQuant as modified on November 01, 2017.

Key customization include accommodating the custom modifications under valid assumptions.
17 changes: 12 additions & 5 deletions pyquant/worker.py
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Expand Up @@ -4,7 +4,7 @@
import copy
import operator
import traceback

import re
from functools import cmp_to_key

import pandas as pd
Expand Down Expand Up @@ -341,22 +341,29 @@ def quantify_peaks(self, params):
else:
if peptide:
for label_mass, label_masses in silac_masses.items():
added_residues = added_residues.union(label_masses)
# labels = [label_mass for mod_aa in peptide if mod_aa in label_masses]
# Replaced above line to look for terminal amino acid modifications status mass difference
labels = 0
for mod_aa in peptide:
if mod_aa in label_masses:
labels += label_mass
for l_masses in label_masses:
if len(l_masses) > 1 and re.search(l_masses, peptide):
labels += label_mass
if 'X' in label_masses:
global_mass = label_mass
if ']' in label_masses:
cterm_mass = label_mass
if '[' in label_masses:
nterm_mass = label_mass
added_residues = added_residues.union(label_masses)
labels = [label_mass for mod_aa in peptide if mod_aa in label_masses]
silac_shift += sum(labels)
silac_shift += labels
else:
# no mass, just assume we have one of the labels
silac_shift += mass_keys[0]
if global_mass is not None:
silac_shift += sum([global_mass for mod_aa in peptide if mod_aa not in added_residues])
silac_shift += cterm_mass + nterm_mass

label_mz = precursor + (silac_shift / float(charge))
theo_mz = theor_mass + (silac_shift / float(charge))
precursors[silac_label]['uncalibrated_mz'] = label_mz
Expand Down