public void add_topdown_theoreticals(ProteinWithGoTerms prot, string seq, string accession, double unmodified_mass, int decoy_number, int lysine_count, List <TheoreticalProteoform> new_theoreticals, int ptm_set_counter, Dictionary <double, int> mod_ranks, int added_ptm_penalty)
{
foreach (TopDownProteoform topdown in Sweet.lollipop.topdown_proteoforms.Where(p => prot.AccessionList.Select(a => a.Split('_')[0]).Contains(p.accession.Split('_')[0].Split('-')[0]) &&
p.sequence == seq).OrderBy(t => t.accession).ThenByDescending(t => t.sequence.Length)) //order by gene name then descending sequence length --> order matters for creating theoreticals.
{
if (!new_theoreticals.Any(t => t.ptm_set.same_ptmset(topdown.topdown_ptm_set, true)))
{
//match each td proteoform group to the closest theoretical w/ best explanation.... otherwise make new theoretical proteoform
PtmSet ptm_set = new PtmSet(topdown.topdown_ptm_set.ptm_combination, mod_ranks, added_ptm_penalty);
TheoreticalProteoform t =
new TheoreticalProteoform(
accession + "_P" + ptm_set_counter.ToString(),
prot.FullDescription + "_P" + ptm_set_counter.ToString() + (decoy_number < 0 ? "" : "_DECOY_" + decoy_number.ToString()),
seq,
(prot as ProteinSequenceGroup != null ? (prot as ProteinSequenceGroup).proteinWithGoTermList.ToArray() : new ProteinWithGoTerms[] { prot }),
unmodified_mass,
lysine_count,
ptm_set,
decoy_number < 0,
false,
theoretical_proteins);
t.topdown_theoretical = true;
new_theoreticals.Add(t);
ptm_set_counter++;
}
}
}
public AmbiguousIdentification(int begin, int end, PtmSet ptm_set, ProteoformRelation relation, TheoreticalProteoform theoretical_base, List <Proteoform> linked_proteoform_references)
{
this.begin = begin;
this.end = end;
this.relation = relation;
this.theoretical_base = theoretical_base;
this.ptm_set = ptm_set;
this.linked_proteoform_references = linked_proteoform_references;
}
public bool topdown_bottomup_comparison(ExperimentalProteoform pf1, TheoreticalProteoform pf2_with_allowed_lysines)
{
List <TopDownProteoform> topdown_proteoforms_same_accession = Sweet.lollipop.topdown_proteoforms.Where(td =>
pf2_with_allowed_lysines.ExpandedProteinList.Any(p =>
p.AccessionList.Select(a => a.Split('_')[0].Split('-')[0])
.Contains(td.accession.Split('_')[0].Split('-')[0]))).ToList();
bool good_BU_PSMs = topdown_proteoforms_same_accession.Count > 0 ||
pf2_with_allowed_lysines.bottom_up_PSMs.Count >= Sweet.lollipop.min_bu_peptides;
return(good_BU_PSMs);
}
public static string get_sequence(TheoreticalProteoform t, int begin, int end)
{
string sequence = t.sequence
.Substring(begin < t.begin ? 0 : begin - t.begin,
1 + end - (begin < t.begin ? t.begin : begin));
if (begin < t.begin)
{
sequence = "M" + sequence;
}
return(sequence);
}
public void set_correct_id()
{
if (linked_proteoform_references == null)
{
correct_id = false;
}
else
{
TheoreticalProteoform t = linked_proteoform_references.First() as TheoreticalProteoform;
bool matching_accession = t.ExpandedProteinList.SelectMany(p => p.AccessionList).Select(a => a.Split('_')[0]).Contains(accession.Split('_')[0].Split('-')[0]);
bool same_begin_and_end = begin == topdown_begin && end == topdown_end;
bool same_ptm_set = topdown_ptm_set.same_ptmset(ptm_set, true);
correct_id = matching_accession && same_ptm_set && same_begin_and_end;
}
}
public double calculate_mass_error(TheoreticalProteoform t, PtmSet ptm_set, int begin, int end)
{
string sequence = t.sequence
.Substring(begin < t.begin ? 0 : begin - t.begin,
1 + end - (begin < t.begin ? t.begin : begin));
if (begin < t.begin)
{
sequence = "M" + sequence;
}
double theoretical_mass =
TheoreticalProteoform.CalculateProteoformMass(sequence, ptm_set.ptm_combination);
return(Math.Round(agg_mass - theoretical_mass, 4));
}
public List <ExperimentalProteoform> identify_connected_experimentals(TheoreticalProteoform theoretical_base, int begin, int end, PtmSet ptm_set, List <Proteoform> linked_proteoform_references)
{
List <ExperimentalProteoform> identified = new List <ExperimentalProteoform>();
//do relations first closest to candidate ptmset delta mass, then in order of relation delta mass (need to do in same order every round)
foreach (ProteoformRelation r in relationships.Where(r => r.Accepted).OrderBy(r => r.candidate_ptmset != null ? Math.Abs(r.candidate_ptmset.mass - r.DeltaMass) : r.DeltaMass * 1e6).Distinct().ToList())
{
ExperimentalProteoform e = r.connected_proteoforms.OfType <ExperimentalProteoform>().FirstOrDefault(p => p != this);
if (e == null)
{
continue;
} // Looking at an ET pair, expecting an EE pair
//if (Sweet.lollipop.identify_from_td_nodes && this as TopDownProteoform != null && e as TopDownProteoform != null) continue; //between two TD nodes
double mass_tolerance = modified_mass / 1000000 * Sweet.lollipop.mass_tolerance;
PtmSet with_mod_change = determine_mod_change(e, this, theoretical_base, r, ptm_set, begin, end);
if (with_mod_change == null && Math.Abs(r.peak.DeltaMass) <= mass_tolerance)
{
lock (r) lock (e) lock (this)
{
if (assign_pf_identity(e, ptm_set, begin, end, r, theoretical_base, linked_proteoform_references, true))
{
r.Identification = true;
identified.Add(e);
}
}
continue;
}
if (with_mod_change == null)
{
continue;
}
lock (r) lock (e) lock (this)
{
if (assign_pf_identity(e, with_mod_change, begin, end, r, theoretical_base, linked_proteoform_references, true))
{
r.Identification = true;
identified.Add(e);
}
}
}
return(identified);
}
public ProteoformRelation(Proteoform pf1, Proteoform pf2, ProteoformComparison relation_type, double delta_mass, string current_directory)
{
connected_proteoforms[0] = pf1;
connected_proteoforms[1] = pf2;
RelationType = relation_type;
DeltaMass = delta_mass;
InstanceId = instanceCounter;
lock (SaveState.lollipop) instanceCounter += 1; //Not thread safe
if (CH2 == null || HPO3 == null)
{
Loaders.LoadElements(Path.Combine(current_directory, "elements.dat"));
CH2 = ChemicalFormula.ParseFormula("C1 H2");
HPO3 = ChemicalFormula.ParseFormula("H1 O3 P1");
}
if (SaveState.lollipop.neucode_labeled)
{
lysine_count = pf1.lysine_count;
}
if ((relation_type == ProteoformComparison.ExperimentalTheoretical || relation_type == ProteoformComparison.ExperimentalDecoy) &&
SaveState.lollipop.theoretical_database.possible_ptmset_dictionary.TryGetValue(Math.Round(delta_mass, 1), out List <PtmSet> candidate_sets) &&
pf2 as TheoreticalProteoform != null)
{
TheoreticalProteoform t = pf2 as TheoreticalProteoform;
double mass_tolerance = t.modified_mass / 1000000 * (double)SaveState.lollipop.mass_tolerance;
List <PtmSet> narrower_range_of_candidates = candidate_sets.Where(s => Math.Abs(s.mass - delta_mass) < 0.05).ToList();
candidate_ptmset = t.generate_possible_added_ptmsets(narrower_range_of_candidates, delta_mass, mass_tolerance, SaveState.lollipop.theoretical_database.all_mods_with_mass, t, t.sequence, SaveState.lollipop.mod_rank_first_quartile)
.OrderBy(x => x.ptm_rank_sum + Math.Abs(Math.Abs(x.mass) - Math.Abs(delta_mass)) * 10E-6) // major score: delta rank; tie breaker: deltaM, where it's always less than 1
.FirstOrDefault();
}
// Start the model (0 Da) at the mass defect of CH2 or HPO3 itself, allowing the peak width tolerance on either side
double half_peak_width = RelationType == ProteoformComparison.ExperimentalTheoretical || RelationType == ProteoformComparison.ExperimentalDecoy ?
SaveState.lollipop.peak_width_base_et / 2 :
SaveState.lollipop.peak_width_base_ee / 2;
double low_decimal_bound = half_peak_width + ((CH2.MonoisotopicMass - Math.Truncate(CH2.MonoisotopicMass)) / CH2.MonoisotopicMass) * (Math.Abs(delta_mass) <= CH2.MonoisotopicMass ? CH2.MonoisotopicMass : Math.Abs(delta_mass));
double high_decimal_bound = 1 - half_peak_width + ((HPO3.MonoisotopicMass - Math.Ceiling(HPO3.MonoisotopicMass)) / HPO3.MonoisotopicMass) * (Math.Abs(delta_mass) <= HPO3.MonoisotopicMass ? HPO3.MonoisotopicMass : Math.Abs(delta_mass));
double delta_mass_decimal = Math.Abs(delta_mass - Math.Truncate(delta_mass));
outside_no_mans_land = delta_mass_decimal <= low_decimal_bound || delta_mass_decimal >= high_decimal_bound ||
high_decimal_bound <= low_decimal_bound;
}
public List <ExperimentalProteoform> identify_connected_experimentals()
{
List <ExperimentalProteoform> identified = new List <ExperimentalProteoform>();
//do relations first closest to candidate ptmset delta mass, then in order of relation delta mass (need to do in same order every round)
foreach (ProteoformRelation r in relationships.Where(r => r.Accepted).OrderBy(r => r.candidate_ptmset != null ? Math.Abs(r.candidate_ptmset.mass - r.DeltaMass) : r.DeltaMass * 1e6).Distinct().ToList())
{
ExperimentalProteoform e = r.connected_proteoforms.OfType <ExperimentalProteoform>().FirstOrDefault(p => p != this);
if (e == null)
{
continue;
} // Looking at an ET pair, expecting an EE pair
TheoreticalProteoform theoretical_base = this as TheoreticalProteoform != null ?
this as TheoreticalProteoform : //Theoretical starting point
(linked_proteoform_references.First() as TheoreticalProteoform != null ?
linked_proteoform_references.First() as TheoreticalProteoform : //Experimental with theoretical reference
null); //Experimental without theoretical reference
double mass_tolerance = modified_mass / 1000000 * Sweet.lollipop.mass_tolerance;
PtmSet with_mod_change = determine_mod_change(e, this, theoretical_base, r, this.ptm_set);
if (with_mod_change == null && Math.Abs(r.peak.DeltaMass) <= mass_tolerance)
{
lock (r) lock (e) assign_pf_identity(e, ptm_set, r, theoretical_base);
identified.Add(e);
}
if (with_mod_change == null)
{
continue;
}
lock (r) lock (e)
assign_pf_identity(e, with_mod_change, r, theoretical_base);
identified.Add(e);
}
return(identified);
}
public List <ExperimentalProteoform> identify_connected_experimentals(List <PtmSet> all_possible_ptmsets, List <ModificationWithMass> all_mods_with_mass)
{
List <ExperimentalProteoform> identified = new List <ExperimentalProteoform>();
foreach (ProteoformRelation r in relationships.Where(r => r.Accepted).Distinct().ToList())
{
ExperimentalProteoform e = r.connected_proteoforms.OfType <ExperimentalProteoform>().FirstOrDefault(p => p != this);
if (e == null)
{
continue; // Looking at an ET pair, expecting an EE pair
}
double mass_tolerance = modified_mass / 1000000 * (double)SaveState.lollipop.mass_tolerance;
int sign = Math.Sign(e.modified_mass - modified_mass);
double deltaM = Math.Sign(r.peak.DeltaMass) < 0 ? r.peak.DeltaMass : sign * r.peak.DeltaMass; // give EE relations the correct sign, but don't switch negative ET relation deltaM's
TheoreticalProteoform theoretical_base = this as TheoreticalProteoform != null ?
this as TheoreticalProteoform : //Theoretical starting point
(linked_proteoform_references.First() as TheoreticalProteoform != null ?
linked_proteoform_references.First() as TheoreticalProteoform : //Experimental with theoretical reference
null); //Experimental without theoretical reference
string theoretical_base_sequence = theoretical_base != null ? theoretical_base.sequence : "";
PtmSet best_addition = generate_possible_added_ptmsets(r.peak.possiblePeakAssignments, deltaM, mass_tolerance, all_mods_with_mass, theoretical_base, theoretical_base_sequence, 1)
.OrderBy(x => (double)x.ptm_rank_sum + Math.Abs(x.mass - deltaM) * 10E-6) // major score: delta rank; tie breaker: deltaM, where it's always less than 1
.FirstOrDefault();
PtmSet best_loss = null;
foreach (PtmSet set in all_possible_ptmsets)
{
bool within_loss_tolerance = deltaM >= -set.mass - mass_tolerance && deltaM <= -set.mass + mass_tolerance;
var these_mods = this.ptm_set.ptm_combination.Select(ptm => ptm.modification);
var those_mods = set.ptm_combination.Select(ptm => ptm.modification); // all must be in the current set to remove them
bool can_be_removed = those_mods.All(m => these_mods.Contains(m));
bool better_than_current_best_loss = best_loss == null || Math.Abs(deltaM - (-set.mass)) < Math.Abs(deltaM - (-best_loss.mass));
if (can_be_removed && within_loss_tolerance && better_than_current_best_loss)
{
best_loss = set;
}
}
// If they're the same and someone hasn't labeled 0 difference with a "ModificationWithMass", then label it null
if (best_addition == null && best_loss == null && Math.Abs(r.peak.DeltaMass) <= mass_tolerance)
{
lock (r) lock (e) assign_pf_identity(e, this, ptm_set, r, sign, null);
identified.Add(e);
}
if (best_addition == null && best_loss == null)
{
continue;
}
// Make the new ptmset with ptms removed or added
PtmSet with_mod_change = null;
if (best_loss == null)
{
with_mod_change = new PtmSet(new List <Ptm>(this.ptm_set.ptm_combination.Concat(best_addition.ptm_combination).Where(ptm => ptm.modification.monoisotopicMass != 0).ToList()));
}
else
{
List <Ptm> new_combo = new List <Ptm>(this.ptm_set.ptm_combination);
foreach (Ptm ptm in best_loss.ptm_combination)
{
new_combo.Remove(new_combo.FirstOrDefault(asdf => asdf.modification == ptm.modification));
}
with_mod_change = new PtmSet(new_combo);
}
lock (r) lock (e)
assign_pf_identity(e, this, with_mod_change, r, sign, best_loss != null ? best_loss : best_addition);
identified.Add(e);
}
return(identified);
}
public List <PtmSet> generate_possible_added_ptmsets(List <PtmSet> possible_peak_assignments, double deltaM, double mass_tolerance, List <ModificationWithMass> all_mods_with_mass,
TheoreticalProteoform theoretical_base, string theoretical_base_sequence, int additional_ptm_penalty)
{
List <ModificationWithMass> known_mods = theoretical_base.ExpandedProteinList.SelectMany(p => p.OneBasedPossibleLocalizedModifications.ToList()).SelectMany(kv => kv.Value).OfType <ModificationWithMass>().ToList();
List <PtmSet> possible_ptmsets = new List <PtmSet>();
int n_terminal_degraded_aas = degraded_aas_count(theoretical_base_sequence, ptm_set, true);
int c_terminal_degraded_aas = degraded_aas_count(theoretical_base_sequence, ptm_set, false);
foreach (PtmSet set in possible_peak_assignments)
{
List <ModificationWithMass> mods_in_set = set.ptm_combination.Select(ptm => ptm.modification).ToList();
int rank_sum = additional_ptm_penalty * (set.ptm_combination.Sum(m => SaveState.lollipop.theoretical_database.unlocalized_lookup.TryGetValue(m.modification, out UnlocalizedModification x) ? x.ptm_count : 1) - 1); // penalize additional PTMs
foreach (ModificationWithMass m in mods_in_set)
{
int mod_rank = SaveState.lollipop.theoretical_database.unlocalized_lookup.TryGetValue(m, out UnlocalizedModification u) ? u.ptm_rank : SaveState.lollipop.modification_ranks[m.monoisotopicMass];
if (m.monoisotopicMass == 0)
{
rank_sum += mod_rank;
continue;
}
bool could_be_m_retention = m.modificationType == "AminoAcid" && m.motif.Motif == "M" && theoretical_base.begin == 2 && !ptm_set.ptm_combination.Select(p => p.modification).Contains(m);
bool motif_matches_n_terminus = n_terminal_degraded_aas < theoretical_base_sequence.Length && m.motif.Motif == theoretical_base_sequence[n_terminal_degraded_aas].ToString();
bool motif_matches_c_terminus = c_terminal_degraded_aas < theoretical_base_sequence.Length && m.motif.Motif == theoretical_base_sequence[theoretical_base_sequence.Length - c_terminal_degraded_aas - 1].ToString();
bool cannot_be_degradation = !motif_matches_n_terminus && !motif_matches_c_terminus;
if (m.modificationType == "Missing" && cannot_be_degradation ||
m.modificationType == "AminoAcid" && !could_be_m_retention ||
u != null ? u.require_proteoform_without_mod : false && set.ptm_combination.Count > 1)
{
rank_sum = Int32.MaxValue;
break;
}
bool could_be_n_term_degradation = m.modificationType == "Missing" && motif_matches_n_terminus;
bool could_be_c_term_degradation = m.modificationType == "Missing" && motif_matches_c_terminus;
bool likely_cleavage_site = could_be_n_term_degradation && SaveState.lollipop.likely_cleavages.Contains(theoretical_base_sequence[n_terminal_degraded_aas].ToString()) ||
could_be_c_term_degradation && SaveState.lollipop.likely_cleavages.Contains(theoretical_base_sequence[theoretical_base_sequence.Length - c_terminal_degraded_aas - 1].ToString());
rank_sum -= Convert.ToInt32(SaveState.lollipop.theoretical_database.variableModifications.Contains(m)); // favor variable modifications over regular modifications of the same mass
// In order of likelihood:
// 1. First, we observe I/L/A cleavage to be the most common,
// 1. "Fatty Acid" is a list of modifications prevalent in yeast or bacterial analysis,
// 1. and unlocalized modifications are a subset of modifications in the intact_mods.txt list that should be included in intact analysis (handled in unlocalized modification)
// 2. Second, other degradations and methionine cleavage are weighted mid-level
// 3. Missed monoisotopic errors are considered, but weighted towards the bottom. This should allow missed monoisotopics with common modifications like oxidation, but not rare ones. (handled in unlocalized modification)
if (likely_cleavage_site)
{
rank_sum += SaveState.lollipop.mod_rank_first_quartile / 2;
}
else if (could_be_m_retention || could_be_n_term_degradation || could_be_c_term_degradation)
{
rank_sum += SaveState.lollipop.mod_rank_second_quartile;
}
else
{
rank_sum += known_mods.Concat(SaveState.lollipop.theoretical_database.variableModifications).Contains(m) ?
mod_rank :
mod_rank + SaveState.lollipop.mod_rank_first_quartile / 2; // Penalize modifications that aren't known for this protein and push really rare ones out of the running if they're not in the protein entry
}
}
if (rank_sum <= SaveState.lollipop.mod_rank_sum_threshold)
{
PtmSet adjusted_ranksum = new PtmSet(set.ptm_combination);
adjusted_ranksum.ptm_rank_sum = rank_sum;
possible_ptmsets.Add(adjusted_ranksum);
}
}
return(possible_ptmsets);
}
private bool assign_pf_identity(ExperimentalProteoform e, PtmSet set, int begin, int end, ProteoformRelation r, TheoreticalProteoform theoretical_base, List <Proteoform> linked_proteoform_references, bool check_ambiguous_IDs)
{
bool identification_assigned = false;
if (!Sweet.lollipop.id_use_ppm_tolerance || Math.Abs(e.calculate_mass_error(theoretical_base, set, begin, end) * 1e6 / e.modified_mass) < Sweet.lollipop.id_ppm_tolerance)
{
int new_begin = begin;
int new_end = end;
PtmSet new_set = new PtmSet(new List <Ptm>(set.ptm_combination));
List <Ptm> remove = new List <Ptm>();
//do retention of M first
foreach (var mod in new_set.ptm_combination.Where(m => m.modification.ModificationType == "AminoAcid"))
{
new_begin--;
remove.Add(mod);
}
foreach (var mod in new_set.ptm_combination.Where(m => m.modification.ModificationType == "Missing"))
{
if (!new_set.ptm_combination.Any(m => m.modification.ModificationType == "AminoAcid") && begin >= theoretical_base.begin)
{
if (theoretical_base.sequence[begin - theoretical_base.begin].ToString() ==
mod.modification.Target.ToString())
{
new_begin++;
remove.Add(mod); //dont have in ptmset --> change the begin & end
}
}
if (!remove.Contains(mod) && theoretical_base.sequence[end - theoretical_base.begin].ToString() ==
mod.modification.Target.ToString())
{
new_end--;
remove.Add(mod);
}
}
foreach (var ptm in remove)
{
new_set.ptm_combination.Remove(ptm);
}
new_set = new PtmSet(new_set.ptm_combination);
if (e.linked_proteoform_references == null)
{
identification_assigned = true;
if (linked_proteoform_references != null)
{
e.linked_proteoform_references = new List <Proteoform>(linked_proteoform_references);
e.linked_proteoform_references.Add(this);
}
else
{
e.linked_proteoform_references = new List <Proteoform>()
{
theoretical_base
};
}
e.relation_to_id = r;
e.ptm_set = new_set;
e.begin = new_begin;
e.end = new_end;
if (e.gene_name == null)
{
e.gene_name = theoretical_base.gene_name;
}
else
{
e.gene_name.gene_names.Concat(this.gene_name.gene_names);
}
}
else
{
if (linked_proteoform_references != null && !linked_proteoform_references.Contains(e))
{
bool different_id = e.gene_name.get_prefered_name(Lollipop.preferred_gene_label) !=
theoretical_base.gene_name.get_prefered_name(Lollipop.preferred_gene_label) ||
ExperimentalProteoform.get_sequence(e.linked_proteoform_references.First() as TheoreticalProteoform, e.begin, e.end)
!= ExperimentalProteoform.get_sequence(theoretical_base, new_begin, new_end) || !e.ptm_set.same_ptmset(new_set, true);
List <Modification> this_known_mods = theoretical_base.ExpandedProteinList.SelectMany(p => p.OneBasedPossibleLocalizedModifications).SelectMany(kv => kv.Value).Where(v => v.MonoisotopicMass != 0).ToList();
List <Modification> previous_id_known_mods = (e.linked_proteoform_references.First() as TheoreticalProteoform).ExpandedProteinList.SelectMany(p => p.OneBasedPossibleLocalizedModifications).SelectMany(kv => kv.Value).Where(v => v.MonoisotopicMass != 0).ToList();
if (!Sweet.lollipop.topdown_theoretical_reduce_ambiguity || (theoretical_base.topdown_theoretical && !(e.linked_proteoform_references.First() as TheoreticalProteoform).topdown_theoretical))
{
if (!Sweet.lollipop.annotated_PTMs_reduce_ambiguity ||
(new_set.ptm_combination.All(mod1 => modification_is_adduct(mod1.modification) || this_known_mods.Select(mod2 => UnlocalizedModification.LookUpId(mod2)).Contains(UnlocalizedModification.LookUpId(mod1.modification))) &&
!e.ptm_set.ptm_combination.All(mod1 => modification_is_adduct(mod1.modification) || previous_id_known_mods.Select(mod2 => UnlocalizedModification.LookUpId(mod2)).Contains(UnlocalizedModification.LookUpId(mod1.modification)))))
{
if (Sweet.lollipop.topdown_theoretical_reduce_ambiguity || Sweet.lollipop.annotated_PTMs_reduce_ambiguity)
{
if (Sweet.lollipop.remove_bad_connections && different_id) //&& e.relation_to_id != r)
{
e.relation_to_id.Identification = false;
e.relation_to_id.represented_ptmset = null;
}
e.linked_proteoform_references = null;
e.ptm_set = new PtmSet(new List <Ptm>());
e.begin = 0;
e.end = 0;
e.gene_name = null;
e.ambiguous_identifications.Clear();
ProteoformRelation relation = null;
e.relation_to_id = relation;
//reassign the topdown - based ID
return(this.assign_pf_identity(e, set, begin, end, r, theoretical_base, linked_proteoform_references, true));
}
}
}
if (Sweet.lollipop.topdown_theoretical_reduce_ambiguity && (e.linked_proteoform_references.First() as TheoreticalProteoform).topdown_theoretical && !theoretical_base.topdown_theoretical)
{
}
else if (Sweet.lollipop.annotated_PTMs_reduce_ambiguity &&
!new_set.ptm_combination.All(mod1 => modification_is_adduct(mod1.modification) || this_known_mods.Select(mod2 => UnlocalizedModification.LookUpId(mod2)).Contains(UnlocalizedModification.LookUpId(mod1.modification))) &&
e.ptm_set.ptm_combination.All(mod1 => modification_is_adduct(mod1.modification) || previous_id_known_mods.Select(mod2 => UnlocalizedModification.LookUpId(mod2)).Contains(UnlocalizedModification.LookUpId(mod1.modification))))
{
}
else
{
if (different_id)
{
var new_linked_proteoform_references = new List <Proteoform>(linked_proteoform_references);
new_linked_proteoform_references.Add(this);
AmbiguousIdentification new_id =
new AmbiguousIdentification(new_begin, new_end, new_set, r, theoretical_base, new_linked_proteoform_references);
lock (e.ambiguous_identifications)
{
if (!e.ambiguous_identifications.Any(p =>
p.theoretical_base.gene_name.primary ==
new_id.theoretical_base.gene_name.primary &&
ExperimentalProteoform.get_sequence(p.theoretical_base, p.begin, p.end) == ExperimentalProteoform.get_sequence(new_id.theoretical_base, new_id.begin, new_id.end) &&
p.ptm_set.same_ptmset(new_id.ptm_set, true)))
{
e.ambiguous_identifications.Add(new_id);
identification_assigned = true;
}
}
}
}
}
}
}
if (check_ambiguous_IDs)
{
//remove bad relations if using td to reduce ambiguity
if (identification_assigned)
{
List <AmbiguousIdentification> to_remove = new List <AmbiguousIdentification>();
List <Modification> previous_id_known_mods = (e.linked_proteoform_references.First() as TheoreticalProteoform).ExpandedProteinList.SelectMany(p => p.OneBasedPossibleLocalizedModifications).SelectMany(kv => kv.Value).Where(m => m.MonoisotopicMass != 0).ToList();
if (theoretical_base.topdown_theoretical && Sweet.lollipop.topdown_theoretical_reduce_ambiguity)
{
to_remove.AddRange(e.ambiguous_identifications.Where(id => !id.theoretical_base.topdown_theoretical));
}
if (Sweet.lollipop.annotated_PTMs_reduce_ambiguity &&
e.ptm_set.ptm_combination.All(mod1 => modification_is_adduct(mod1.modification) || previous_id_known_mods.Select(mod2 => UnlocalizedModification.LookUpId(mod2)).Contains(UnlocalizedModification.LookUpId(mod1.modification))))
{
foreach (var ambiguous_id in e.ambiguous_identifications)
{
List <Modification> ambiguous_id_known_mods = ambiguous_id.theoretical_base.ExpandedProteinList.SelectMany(p => p.OneBasedPossibleLocalizedModifications).SelectMany(kv => kv.Value).Where(m => m.MonoisotopicMass != 0).ToList();
if (ambiguous_id.ptm_set.ptm_combination.Any(mod1 => !modification_is_adduct(mod1.modification) && !ambiguous_id_known_mods.Select(mod2 => UnlocalizedModification.LookUpId(mod2)).Contains(UnlocalizedModification.LookUpId(mod1.modification))))
{
to_remove.Add(ambiguous_id);
}
}
}
foreach (var x in to_remove)
{
if (e.ambiguous_identifications.Contains(x))
{
e.ambiguous_identifications.Remove(x);
if (Sweet.lollipop.remove_bad_connections)
{
if (e.relation_to_id != x.relation)
{
x.relation.Identification = false;
x.relation.represented_ptmset = null;
}
}
}
}
foreach (var x in e.ambiguous_identifications)
{
x.relation.Identification = true;
}
}
if (this as ExperimentalProteoform != null && (this as ExperimentalProteoform).ambiguous_identifications.Count > 0)
{
lock ((this as ExperimentalProteoform).ambiguous_identifications)
{
int count = (this as ExperimentalProteoform).ambiguous_identifications.Count;
PtmSet[] new_ptm_set = new PtmSet[count];
Parallel.For(0, count, i =>
{
var id = (this as ExperimentalProteoform).ambiguous_identifications[i];
new_ptm_set[i] = determine_mod_change(e, this, id.theoretical_base, r, id.ptm_set, id.begin, id.end);
});
for (int i = 0; i < count; i++)
{
if (new_ptm_set[i] != null)
{
var id = (this as ExperimentalProteoform).ambiguous_identifications[i];
if (assign_pf_identity(e, new_ptm_set[i], id.begin, id.end, r, id.theoretical_base, id.linked_proteoform_references, false))
{
identification_assigned = true;
}
}
}
}
}
}
return(identification_assigned);
}
public static List <PtmSet> generate_possible_added_ptmsets(List <PtmSet> possible_peak_assignments, List <Modification> all_mods_with_mass,
TheoreticalProteoform theoretical_base, int begin, int end, PtmSet ptm_set, int additional_ptm_penalty, bool final_assignment)
{
List <Modification> known_mods = theoretical_base.ExpandedProteinList.SelectMany(p => p.OneBasedPossibleLocalizedModifications).SelectMany(kv => kv.Value).ToList();
List <PtmSet> possible_ptmsets = new List <PtmSet>();
foreach (PtmSet set in possible_peak_assignments)
{
List <Modification> mods_in_set = set.ptm_combination.Select(ptm => ptm.modification).ToList();
int rank_sum = additional_ptm_penalty * (set.ptm_combination.Sum(m => Sweet.lollipop.theoretical_database.unlocalized_lookup.TryGetValue(m.modification, out UnlocalizedModification x) ? x.ptm_count : 1) - 1); // penalize additional PTMs
foreach (Modification m in mods_in_set)
{
int mod_rank = Sweet.lollipop.theoretical_database.unlocalized_lookup.TryGetValue(m, out UnlocalizedModification u) ? u.ptm_rank : Sweet.lollipop.modification_ranks.TryGetValue(Math.Round((double)m.MonoisotopicMass, 5), out int x) ? x : Sweet.lollipop.mod_rank_sum_threshold;
bool could_be_m_retention = m.ModificationType == "AminoAcid" && m.Target.ToString() == "M" && theoretical_base.begin == 2 && begin == 2 && !ptm_set.ptm_combination.Any(p => p.modification.Equals(m));
bool motif_matches_n_terminus = begin - theoretical_base.begin >= 0 && begin - theoretical_base.begin < theoretical_base.sequence.Length && m.Target.ToString() == theoretical_base.sequence[begin - theoretical_base.begin].ToString() && !mods_in_set.Any(mod => mod.ModificationType == "AminoAcid" && mod.Target.ToString() == "M");
bool motif_matches_c_terminus = end - theoretical_base.begin >= 0 && end - theoretical_base.begin < theoretical_base.sequence.Length && m.Target.ToString() == theoretical_base.sequence[end - theoretical_base.begin].ToString();
bool cannot_be_degradation = !motif_matches_n_terminus && !motif_matches_c_terminus;
if ((m.ModificationType == "Missing" && cannot_be_degradation) ||
(m.ModificationType == "AminoAcid" && !could_be_m_retention) ||
((u != null ? u.require_proteoform_without_mod : false) && set.ptm_combination.Count > 1))
{
rank_sum = Int32.MaxValue;
break;
}
bool could_be_n_term_degradation = m.ModificationType == "Missing" && motif_matches_n_terminus;
bool could_be_c_term_degradation = m.ModificationType == "Missing" && motif_matches_c_terminus;
//if selected, going to only allow mods in Mods folder (type "Common"), Missing, Missed Monoisotopic, known mods for that protein, or Unmodified
if (Sweet.lollipop.only_assign_common_or_known_mods && final_assignment)
{
if (!(m.MonoisotopicMass == 0 || m.ModificationType == "Common" || could_be_m_retention || could_be_n_term_degradation || could_be_c_term_degradation || m.ModificationType == "Deconvolution Error" || known_mods.Concat(Sweet.lollipop.theoretical_database.variableModifications).Contains(m) ||
known_mods.Select(mod => UnlocalizedModification.LookUpId(mod)).Contains(UnlocalizedModification.LookUpId(m))))
{
rank_sum = Int32.MaxValue;
break;
}
}
// In order of likelihood:
// 1. First, we observe I/L/A cleavage to be the most common, other degradations and methionine cleavage are weighted mid-level
// 2. Missed monoisotopic errors are considered, but weighted towards the bottom. This should allow missed monoisotopics with common modifications like oxidation, but not rare ones. (handled in unlocalized modification)
if (m.MonoisotopicMass == 0)
{
rank_sum += mod_rank;
continue;
}
rank_sum -= Convert.ToInt32(Sweet.lollipop.theoretical_database.variableModifications.Contains(m)); // favor variable modifications over regular modifications of the same mass
if (could_be_m_retention || could_be_n_term_degradation || could_be_c_term_degradation)
{
rank_sum += Sweet.lollipop.mod_rank_first_quartile / 2;
}
else if (m.ModificationType == "Deconvolution Error")
{
rank_sum += Sweet.lollipop.neucode_labeled ?
Sweet.lollipop.mod_rank_third_quartile : //in neucode-labeled data, fewer missed monoisotopics - don't prioritize
1; //in label-free, more missed monoisotoipcs, should prioritize (set to same priority as variable modification)
rank_sum -= additional_ptm_penalty;
}
else
{
//if annotated in DB for this, just add 1?
rank_sum += known_mods.Concat(Sweet.lollipop.theoretical_database.variableModifications).Select(mod => UnlocalizedModification.LookUpId(mod)).Contains(UnlocalizedModification.LookUpId(m))
?
1 : //mod rank
mod_rank + Sweet.lollipop.mod_rank_first_quartile / 2; // Penalize modifications that aren't known for this protein and push really rare ones out of the running if they're not in the protein entry
}
}
if (rank_sum <= Sweet.lollipop.mod_rank_sum_threshold)
{
PtmSet adjusted_ranksum = new PtmSet(set.ptm_combination);
adjusted_ranksum.ptm_rank_sum = rank_sum;
possible_ptmsets.Add(adjusted_ranksum);
}
}
return(possible_ptmsets);
}
private static PtmSet determine_mod_change(ExperimentalProteoform e, Proteoform p,
TheoreticalProteoform theoretical_base, ProteoformRelation r, PtmSet this_ptmset, int begin, int end)
{
double mass_tolerance = p.modified_mass / 1000000 * Sweet.lollipop.mass_tolerance;
int sign = Math.Sign(e.modified_mass - p.modified_mass);
double deltaM =
Math.Sign(r.peak.DeltaMass) < 0
? r.peak.DeltaMass
: sign * r.peak
.DeltaMass; // give EE relations the correct sign, but don't switch negative ET relation deltaM's
List <PtmSet> possible_additions = r.peak.possiblePeakAssignments
.Where(peak => Math.Abs(peak.mass - deltaM) <= 1)
.ToList(); // EE relations have PtmSets around both positive and negative deltaM, so remove the ones around the opposite of the deltaM of interest
PtmSet best_addition = generate_possible_added_ptmsets(possible_additions,
Sweet.lollipop.theoretical_database.all_mods_with_mass, theoretical_base, begin, end,
this_ptmset, 1, true)
.OrderBy(x =>
(double)x.ptm_rank_sum +
Math.Abs(x.mass - deltaM) *
10E-6) // major score: delta rank; tie breaker: deltaM, where it's always less than 1
.FirstOrDefault();
List <PtmSet> best_losses = new List <PtmSet>();
foreach (PtmSet set in r.peak.possiblePeakAssignments)
//Parallel.ForEach(Sweet.lollipop.theoretical_database.all_possible_ptmsets, set =>
{
bool within_loss_tolerance = deltaM >= -set.mass - mass_tolerance && deltaM <= -set.mass + mass_tolerance;
if (within_loss_tolerance)
{
List <Modification> these_mods = this_ptmset.ptm_combination.Select(ptm => ptm.modification).ToList();
List <Modification> those_mods = set.ptm_combination.Select(ptm => ptm.modification).ToList(); // all must be in the current set to remove them
bool can_be_removed = those_mods.All(m1 => these_mods.Count(m2 =>
UnlocalizedModification.LookUpId(m2) ==
UnlocalizedModification.LookUpId(m1)) >=
those_mods.Count(m2 =>
UnlocalizedModification.LookUpId(m2) ==
UnlocalizedModification.LookUpId(m1)));
lock (best_losses)
{
if (can_be_removed && within_loss_tolerance)
{
best_losses.Add(set);
}
}
}
} //);
PtmSet best_loss = best_losses.OrderBy(s => Math.Abs(deltaM - (-s.mass))).FirstOrDefault();
if (best_addition == null && best_loss == null)
{
return(null);
}
// Make the new ptmset with ptms removed or added
PtmSet with_mod_change = null;
if (best_loss == null)
{
with_mod_change = new PtmSet(new List <Ptm>(this_ptmset.ptm_combination
.Concat(best_addition.ptm_combination).Where(ptm => ptm.modification.MonoisotopicMass != 0)
.ToList()));
}
else
{
List <Ptm> new_combo = new List <Ptm>(this_ptmset.ptm_combination);
foreach (Ptm ptm in best_loss.ptm_combination)
{
new_combo.Remove(new_combo.FirstOrDefault(asdf => UnlocalizedModification.LookUpId(asdf.modification) == UnlocalizedModification.LookUpId(ptm.modification)));
}
with_mod_change = new PtmSet(new_combo);
}
if (r.represented_ptmset == null)
{
r.represented_ptmset = best_loss == null ? best_addition : best_loss;
//if (r.RelationType == ProteoformComparison.ExperimentalExperimental)
//{
// r.DeltaMass *= sign;
//}
}
return(with_mod_change);
}
private void assign_pf_identity(ExperimentalProteoform e, PtmSet set, ProteoformRelation r, TheoreticalProteoform theoretical_base)
{
if (e.linked_proteoform_references == null)
{
e.linked_proteoform_references = new List <Proteoform>(this.linked_proteoform_references);
e.linked_proteoform_references.Add(this);
e.ptm_set = set;
e.begin = this.begin;
e.end = this.end;
List <Ptm> remove = new List <Ptm>();
//do retention of M first
foreach (var mod in set.ptm_combination.Where(m => m.modification.ModificationType == "AminoAcid"))
{
e.begin--;
remove.Add(mod);
}
foreach (var mod in set.ptm_combination.Where(m => m.modification.ModificationType == "Missing"))
{
if (theoretical_base.sequence[this.begin - theoretical_base.begin].ToString() == mod.modification.Target.ToString())
{
e.begin++;
remove.Add(mod); //dont have in ptmset --> change the begin & end
}
else if (theoretical_base.sequence[this.end - this.begin].ToString() == mod.modification.Target.ToString())
{
e.end--;
remove.Add(mod);
}
}
foreach (var ptm in remove)
{
e.ptm_set.ptm_combination.Remove(ptm);
}
e.ptm_set = new PtmSet(e.ptm_set.ptm_combination);
if (e.gene_name == null)
{
e.gene_name = this.gene_name;
}
else if (!e.topdown_id)
{
e.gene_name.gene_names.Concat(this.gene_name.gene_names);
}
}
else
{
//check if assign
int begin = this.begin;
int end = this.end;
PtmSet ptm_set = set;
List <Ptm> remove = new List <Ptm>();
//do retention of M first
foreach (var mod in set.ptm_combination.Where(m => m.modification.ModificationType == "AminoAcid"))
{
begin--;
remove.Add(mod);
}
foreach (var mod in set.ptm_combination.Where(m => m.modification.ModificationType == "Missing"))
{
if (theoretical_base.sequence[this.begin - theoretical_base.begin].ToString() ==
mod.modification.Target.ToString())
{
begin++;
remove.Add(mod); //dont have in ptmset --> change the begin & end
}
else if (theoretical_base.sequence[this.end - this.begin].ToString() ==
mod.modification.Target.ToString())
{
end--;
remove.Add(mod);
}
}
foreach (var ptm in remove)
{
ptm_set.ptm_combination.Remove(ptm);
}
ptm_set = new PtmSet(ptm_set.ptm_combination);
if (e.gene_name.get_prefered_name(Lollipop.preferred_gene_label) !=
this.gene_name.get_prefered_name(Lollipop.preferred_gene_label) ||
e.begin != begin || e.end != end || !e.ptm_set.same_ptmset(ptm_set, true))
{
e.ambiguous = true;
Proteoform linked_proteoform_reference =
this.linked_proteoform_references == null || this.linked_proteoform_references.Count == 0
? this
: this.linked_proteoform_references.First();
Tuple <Proteoform, int, int, PtmSet> new_id =
new Tuple <Proteoform, int, int, PtmSet>(linked_proteoform_reference, begin, end, ptm_set);
lock (e.ambiguous_identifications)
{
if (!e.ambiguous_identifications.Any(p =>
p.Item1.gene_name.get_prefered_name(Lollipop.preferred_gene_label) ==
new_id.Item1.gene_name.get_prefered_name(Lollipop.preferred_gene_label) &&
p.Item2 == new_id.Item2 && p.Item3 == new_id.Item3 &&
p.Item4.same_ptmset(new_id.Item4, true)))
{
e.ambiguous_identifications.Add(new_id);
}
}
}
}
if (this as ExperimentalProteoform != null && (this as ExperimentalProteoform).ambiguous)
{
foreach (var id in this.ambiguous_identifications)
{
TheoreticalProteoform id_theoretical_base = id.Item1 as TheoreticalProteoform;
int begin = id.Item2;
int end = id.Item3;
var remove = new List <Ptm>();
var ptm_set = determine_mod_change(e, this, id_theoretical_base, r, id.Item4);
if (ptm_set == null)
{
continue;
}
//do retention of M first
foreach (var mod in ptm_set.ptm_combination.Where(m => m.modification.ModificationType == "AminoAcid"))
{
begin--;
remove.Add(mod);
}
foreach (var mod in ptm_set.ptm_combination.Where(m => m.modification.ModificationType == "Missing"))
{
if (id_theoretical_base.sequence[id.Item2 - id.Item1.begin].ToString() == mod.modification.Target.ToString())
{
begin++;
remove.Add(mod); //dont have in ptmset --> change the begin & end
}
else if (id_theoretical_base.sequence[id.Item3 - id.Item2].ToString() == mod.modification.Target.ToString())
{
end--;
remove.Add(mod);
}
}
foreach (var ptm in remove)
{
ptm_set.ptm_combination.Remove(ptm);
}
ptm_set = new PtmSet(ptm_set.ptm_combination);
lock (e.ambiguous_identifications)
{
var new_id = new Tuple <Proteoform, int, int, PtmSet>(id.Item1, begin, end, ptm_set);
if ((e.gene_name.get_prefered_name(Lollipop.preferred_gene_label) !=
new_id.Item1.gene_name.get_prefered_name(Lollipop.preferred_gene_label) ||
e.begin != new_id.Item2 || e.end != new_id.Item3 || !e.ptm_set.same_ptmset(new_id.Item4, true)) &&
!e.ambiguous_identifications.Any(p =>
p.Item1.gene_name.get_prefered_name(Lollipop.preferred_gene_label) ==
new_id.Item1.gene_name.get_prefered_name(Lollipop.preferred_gene_label) &&
p.Item2 == new_id.Item2 && p.Item3 == new_id.Item3 &&
p.Item4.same_ptmset(new_id.Item4, true)))
{
e.ambiguous_identifications.Add(new_id);
e.ambiguous = true;
}
}
}
}
e.uniprot_mods = "";
foreach (string mod in e.ptm_set.ptm_combination.Concat(e.ambiguous_identifications.SelectMany(i => i.Item4.ptm_combination)).Where(ptm => ptm.modification.ModificationType != "Deconvolution Error").Select(ptm => UnlocalizedModification.LookUpId(ptm.modification)).ToList().Distinct().OrderBy(m => m))
{
// positions with mod
List <int> theo_ptms = theoretical_base.ExpandedProteinList.First()
.OneBasedPossibleLocalizedModifications
.Where(p => p.Key >= e.begin && p.Key <= e.end &&
p.Value.Select(m => UnlocalizedModification.LookUpId(m)).Contains(mod))
.Select(m => m.Key).ToList();
if (theo_ptms.Count > 0)
{
e.uniprot_mods += mod + " @ " + string.Join(", ", theo_ptms) + "; ";
}
if (e.ptm_set.ptm_combination.Select(ptm => UnlocalizedModification.LookUpId(ptm.modification))
.Count(m => m == mod) > theo_ptms.Count ||
e.ambiguous_identifications.Any(i => i.Item4.ptm_combination.Select(ptm => UnlocalizedModification.LookUpId(ptm.modification))
.Count(m => m == mod) > theo_ptms.Count))
{
e.novel_mods = true;
}
}
//else if (!e.topdown_id && e.gene_name.get_prefered_name(Lollipop.preferred_gene_label) != this.gene_name.get_prefered_name(Lollipop.preferred_gene_label)
// && e.linked_proteoform_references.Count == this.linked_proteoform_references.Count + 1)
//{
// e.ambiguous = true;
//}
}
public void EnterTheoreticalProteformFamily(string seq, ProteinWithGoTerms prot, IDictionary <int, List <Modification> > modifications, string accession, List <TheoreticalProteoform> theoretical_proteoforms, int decoy_number, IEnumerable <Modification> variableModifications)
{
List <TheoreticalProteoform> new_theoreticals = new List <TheoreticalProteoform>();
if (seq.Length > 3000 || seq.Any(s => !aaIsotopeMassList.ContainsKey(s)))
{
return;
}
//Calculate the properties of this sequence
double unmodified_mass = TheoreticalProteoform.CalculateProteoformMass(seq, new List <Ptm>());
int lysine_count = seq.Split('K').Length - 1;
bool check_contaminants = theoretical_proteins.Any(item => item.Key.ContaminantDB);
//Figure out the possible ptm sets
Dictionary <int, List <Modification> > possibleLocalizedMods = modifications.ToDictionary(kv => kv.Key, kv => new List <Modification>(kv.Value));
foreach (Modification m in variableModifications)
{
for (int i = 1; i <= prot.BaseSequence.Length; i++)
{
if (prot.BaseSequence[i - 1].ToString() == m.Target.ToString())
{
if (!possibleLocalizedMods.TryGetValue(i, out List <Modification> a))
{
possibleLocalizedMods.Add(i, new List <Modification> {
m
});
}
else
{
a.Add(m);
}
}
}
}
int ptm_set_counter = 1;
//if top-down protein sequence, only add PTMs from that top-down proteoforms (will happen in add_topdown_theoreticals method)
if (!prot.topdown_protein)
{
List <PtmSet> unique_ptm_groups = PtmCombos.get_combinations(possibleLocalizedMods, Sweet.lollipop.max_ptms, Sweet.lollipop.modification_ranks, Sweet.lollipop.mod_rank_first_quartile / 2, limit_triples_and_greater);
//Enumerate the ptm combinations with _P# to distinguish from the counts in ProteinSequenceGroups (_#G) and TheoreticalPfGps (_#T)
foreach (PtmSet ptm_set in unique_ptm_groups)
{
TheoreticalProteoform t =
new TheoreticalProteoform(
accession + "_P" + ptm_set_counter.ToString(),
prot.FullDescription + "_P" + ptm_set_counter.ToString() + (decoy_number < 0 ? "" : "_DECOY_" + decoy_number.ToString()),
seq,
(prot as ProteinSequenceGroup != null ? (prot as ProteinSequenceGroup).proteinWithGoTermList.ToArray() : new ProteinWithGoTerms[] { prot }),
unmodified_mass,
lysine_count,
ptm_set,
decoy_number < 0,
check_contaminants,
theoretical_proteins);
t.topdown_theoretical = prot.topdown_protein;
new_theoreticals.Add(t);
ptm_set_counter++;
}
}
add_topdown_theoreticals(prot, seq, accession, unmodified_mass, decoy_number, lysine_count, new_theoreticals, ptm_set_counter, Sweet.lollipop.modification_ranks, Sweet.lollipop.mod_rank_first_quartile / 2);
lock (theoretical_proteoforms) theoretical_proteoforms.AddRange(new_theoreticals);
}
public ProteoformRelation(Proteoform pf1, Proteoform pf2, ProteoformComparison relation_type, double delta_mass, string current_directory)
{
connected_proteoforms[0] = pf1;
connected_proteoforms[1] = pf2;
RelationType = relation_type;
DeltaMass = delta_mass;
InstanceId = instanceCounter;
lock (Sweet.lollipop) instanceCounter += 1; //Not thread safe
if (CH2 == null || HPO3 == null)
{
CH2 = ChemicalFormula.ParseFormula("C1 H2");
HPO3 = ChemicalFormula.ParseFormula("H1 O3 P1");
}
if (Sweet.lollipop.neucode_labeled)
{
lysine_count = pf1.lysine_count;
}
List <PtmSet> candidate_sets = new List <PtmSet>();
if (Sweet.lollipop.et_use_notch && (relation_type == ProteoformComparison.ExperimentalTheoretical || relation_type == ProteoformComparison.ExperimentalDecoy))
{
if (Sweet.lollipop.et_use_notch && !Sweet.lollipop.et_notch_ppm)
{
double mass = delta_mass - Sweet.lollipop.notch_tolerance_et;
while (mass <= delta_mass + Sweet.lollipop.notch_tolerance_et)
{
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary_notches.TryGetValue(
Math.Round(mass, 1), out List <PtmSet> candidates);
if (candidates != null)
{
candidate_sets.AddRange(candidates);
}
mass += 0.1;
}
candidate_sets = candidate_sets.Distinct().ToList();
}
else
{
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary_notches.TryGetValue(Math.Round(delta_mass, 1), out candidate_sets);
}
if (candidate_sets != null)
{
candidate_sets = candidate_sets.Where(s => Sweet.lollipop.et_notch_ppm
? Math.Abs(s.mass - delta_mass) * 1e6 / pf1.modified_mass <
Sweet.lollipop.notch_tolerance_et
: Math.Abs(s.mass - delta_mass) < Sweet.lollipop.notch_tolerance_et).ToList();
candidate_ptmset = candidate_sets.OrderBy(s => s.ptm_rank_sum).FirstOrDefault();
}
}
else if (Sweet.lollipop.ee_use_notch &&
(relation_type == ProteoformComparison.ExperimentalExperimental ||
relation_type == ProteoformComparison.ExperimentalFalse))
{
if (Sweet.lollipop.ee_use_notch && !Sweet.lollipop.ee_notch_ppm)
{
double mass = delta_mass - Sweet.lollipop.notch_tolerance_ee;
while (mass <= delta_mass + Sweet.lollipop.notch_tolerance_ee)
{
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary_notches.TryGetValue(
Math.Round(mass, 1), out List <PtmSet> candidates);
if (candidates != null)
{
candidate_sets.AddRange(candidates);
}
mass += 0.1;
}
candidate_sets = candidate_sets.Distinct().ToList();
}
else
{
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary_notches.TryGetValue(Math.Round(delta_mass, 1), out candidate_sets);
}
if (candidate_sets != null)
{
candidate_sets = candidate_sets.Where(s => Sweet.lollipop.ee_notch_ppm
? Math.Abs(s.mass - delta_mass) * 1e6 / pf1.modified_mass <
Sweet.lollipop.notch_tolerance_ee
: Math.Abs(s.mass - delta_mass) < Sweet.lollipop.notch_tolerance_ee).ToList();
candidate_ptmset = candidate_sets.OrderBy(s => s.ptm_rank_sum).FirstOrDefault();
}
}
else if
(relation_type == ProteoformComparison.ExperimentalTheoretical ||
relation_type == ProteoformComparison.ExperimentalDecoy)
{
if (Sweet.lollipop.peak_width_base_et > 0.09)
{
double mass = delta_mass - Sweet.lollipop.peak_width_base_et;
while (mass <= delta_mass + Sweet.lollipop.peak_width_base_et)
{
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary.TryGetValue(
Math.Round(mass, 1), out List <PtmSet> candidates);
if (candidates != null)
{
candidate_sets.AddRange(candidates);
}
mass += 0.1;
}
candidate_sets = candidate_sets.Distinct().ToList();
}
else
{
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary.TryGetValue(
Math.Round(delta_mass, 1), out candidate_sets);
}
if (pf2 as TheoreticalProteoform != null && candidate_sets != null && candidate_sets.Count > 0)
{
List <PtmSet> narrower_range_of_candidates = new List <PtmSet>();
if (Sweet.lollipop.et_use_notch)
{
narrower_range_of_candidates = candidate_sets;
}
else
{
narrower_range_of_candidates = candidate_sets
.Where(s => Math.Abs(s.mass - delta_mass) < Sweet.lollipop.peak_width_base_et).ToList();
}
TheoreticalProteoform t = pf2 as TheoreticalProteoform;
candidate_ptmset = Proteoform.generate_possible_added_ptmsets(narrower_range_of_candidates,
Sweet.lollipop.theoretical_database.all_mods_with_mass, t, pf2.begin, pf2.end,
pf2.ptm_set,
Sweet.lollipop.mod_rank_first_quartile, false).OrderBy(x =>
x.ptm_rank_sum +
Math.Abs(Math.Abs(x.mass) - Math.Abs(delta_mass)) *
10E-6) // major score: delta rank; tie breaker: deltaM, where it's always less than 1
.FirstOrDefault();
}
}
// Start the model (0 Da) at the mass defect of CH2 or HPO3 itself, allowing the peak width tolerance on either side
double half_peak_width = RelationType == ProteoformComparison.ExperimentalTheoretical || RelationType == ProteoformComparison.ExperimentalDecoy ?
Sweet.lollipop.peak_width_base_et / 2 :
Sweet.lollipop.peak_width_base_ee / 2;
double low_decimal_bound = half_peak_width + ((CH2.MonoisotopicMass - Math.Truncate(CH2.MonoisotopicMass)) / CH2.MonoisotopicMass) * (Math.Abs(delta_mass) <= CH2.MonoisotopicMass ? CH2.MonoisotopicMass : Math.Abs(delta_mass));
double high_decimal_bound = 1 - half_peak_width + ((HPO3.MonoisotopicMass - Math.Ceiling(HPO3.MonoisotopicMass)) / HPO3.MonoisotopicMass) * (Math.Abs(delta_mass) <= HPO3.MonoisotopicMass ? HPO3.MonoisotopicMass : Math.Abs(delta_mass));
double delta_mass_decimal = Math.Abs(delta_mass - Math.Truncate(delta_mass));
outside_no_mans_land = delta_mass_decimal <= low_decimal_bound || delta_mass_decimal >= high_decimal_bound ||
high_decimal_bound <= low_decimal_bound;
if (Sweet.lollipop.et_use_notch && (relation_type == ProteoformComparison.ExperimentalTheoretical || relation_type == ProteoformComparison.ExperimentalDecoy))
{
outside_no_mans_land = true;
}
if (Sweet.lollipop.ee_use_notch && (relation_type == ProteoformComparison.ExperimentalExperimental || relation_type == ProteoformComparison.ExperimentalFalse))
{
outside_no_mans_land = true;
}
}
public void identify_experimentals()
{
HashSet <ExperimentalProteoform> identified_experimentals = new HashSet <ExperimentalProteoform>();
if (Sweet.lollipop.identify_from_td_nodes)
{
foreach (TopDownProteoform topdown in experimental_proteoforms.Where(e => e.topdown_id))
{
Sweet.lollipop.theoretical_database
.theoreticals_by_accession[Sweet.lollipop.target_proteoform_community.community_number]
.TryGetValue(topdown.accession.Split('_')[0].Split('-')[0], out var t);
if (t != null && t.Count > 0)
{
TheoreticalProteoform theoretical =
new TheoreticalProteoform(topdown.accession, topdown.name, topdown.sequence,
t.First().ExpandedProteinList, topdown.modified_mass, topdown.lysine_count,
topdown.topdown_ptm_set, true, false, null);
theoretical.topdown_theoretical = true;
theoretical.new_topdown_proteoform = true;
theoretical.begin = topdown.topdown_begin;
theoretical.end = topdown.topdown_end;
foreach (ExperimentalProteoform e in topdown.identify_connected_experimentals(theoretical, topdown.topdown_begin, topdown.topdown_end,
new PtmSet(topdown.topdown_ptm_set.ptm_combination), null))
{
identified_experimentals.Add(e);
}
}
}
}
foreach (TheoreticalProteoform t in theoretical_proteoforms.OrderBy(t => t.topdown_theoretical))
{
lock (identified_experimentals)
foreach (ExperimentalProteoform e in t.identify_connected_experimentals(t, t.begin, t.end, t.ptm_set, t.linked_proteoform_references))
{
identified_experimentals.Add(e);
}
}
//Continue looking for new experimental identifications until no more remain to be identified
List <ExperimentalProteoform> newly_identified_experimentals = new List <ExperimentalProteoform>(identified_experimentals).OrderBy(p => p.relationships.Count(r => r.candidate_ptmset != null) > 0 ? p.relationships.Where(r => r.candidate_ptmset != null).Min(r => Math.Abs(r.DeltaMass - r.candidate_ptmset.mass)) : 1e6).ThenBy(p => p.modified_mass).ToList();
int last_identified_count = identified_experimentals.Count - 1;
while (newly_identified_experimentals.Count > 0) //&& identified_experimentals.Count > last_identified_count)
{
last_identified_count = identified_experimentals.Count;
HashSet <ExperimentalProteoform> tmp_new_experimentals = new HashSet <ExperimentalProteoform>();
foreach (ExperimentalProteoform id_experimental in newly_identified_experimentals)
{
{
lock (identified_experimentals) lock (tmp_new_experimentals)
foreach (ExperimentalProteoform new_e in id_experimental.identify_connected_experimentals(id_experimental.linked_proteoform_references.First() as TheoreticalProteoform, id_experimental.begin,
id_experimental.end, id_experimental.ptm_set, id_experimental.linked_proteoform_references))
{
identified_experimentals.Add(new_e);
tmp_new_experimentals.Add(new_e);
}
}
}
newly_identified_experimentals = new List <ExperimentalProteoform>(tmp_new_experimentals);
}
List <string> topdown_ids = Sweet.lollipop.topdown_proteoforms
.Select(p => p.accession.Split('_')[0].Split('-')[0] + "_" + p.sequence + "_" + string.Join(", ", p.topdown_ptm_set.ptm_combination.Where(m => m.modification.ModificationType != "Deconvolution Error").Select(ptm => UnlocalizedModification.LookUpId(ptm.modification)).OrderBy(m => m))).ToList();
//determine identified experimentals that are adducts
//checks if any experimentals have same mods as e's ptmset, except e has additional adduct only mods.
Parallel.ForEach(experimental_proteoforms, e =>
{
e.adduct =
e.linked_proteoform_references != null &&
e.ptm_set.ptm_combination.Any(m => Proteoform.modification_is_adduct(m.modification)) &&
experimental_proteoforms.Any(l =>
l.linked_proteoform_references != null &&
l.gene_name.get_prefered_name(Lollipop.preferred_gene_label) == e.gene_name.get_prefered_name(Lollipop.preferred_gene_label) &&
l.ptm_set.ptm_combination.Count < e.ptm_set.ptm_combination.Count &&
e.ptm_set.ptm_combination.Where(m => l.ptm_set.ptm_combination.Count(p => UnlocalizedModification.LookUpId(p.modification) == UnlocalizedModification.LookUpId(m.modification)) != e.ptm_set.ptm_combination.Count(p => UnlocalizedModification.LookUpId(p.modification) == UnlocalizedModification.LookUpId(m.modification)))
.Count(p => !Proteoform.modification_is_adduct(p.modification))
== 0
);
if (e as TopDownProteoform != null)
{
(e as TopDownProteoform).set_correct_id();
}
if (e.linked_proteoform_references != null)
{
var mods = e.ptm_set.ptm_combination.Where(p => !Proteoform.modification_is_adduct(p.modification))
.Select(ptm => UnlocalizedModification.LookUpId(ptm.modification)).ToList().Distinct().OrderBy(m => m).ToList();
e.uniprot_mods = "";
string add = "";
foreach (string mod in mods)
{
// positions with mod
List <int> theo_ptms = (e.linked_proteoform_references.First() as TheoreticalProteoform).ExpandedProteinList.SelectMany(p => p
.OneBasedPossibleLocalizedModifications)
.Where(p => p.Key >= e.begin && p.Key <= e.end &&
p.Value.Select(m => UnlocalizedModification.LookUpId(m)).Contains(mod))
.Select(m => m.Key).ToList();
if (theo_ptms.Count > 0)
{
add += mod + " @ " + string.Join(", ", theo_ptms) + "; ";
}
if (e.ptm_set.ptm_combination.Where(ptm => ptm.modification.ModificationType != "Deconvolution Error" && !Proteoform.modification_is_adduct(ptm.modification)).Select(ptm => UnlocalizedModification.LookUpId(ptm.modification))
.Count(m => m == mod) > theo_ptms.Count)
{
e.novel_mods = true;
}
}
e.uniprot_mods += add;
if (add.Length == 0)
{
e.uniprot_mods += "N/A";
}
foreach (var ambig_id in e.ambiguous_identifications)
{
var ambig_mods = ambig_id.ptm_set.ptm_combination.Where(p => !Proteoform.modification_is_adduct(p.modification))
.Select(ptm => UnlocalizedModification.LookUpId(ptm.modification)).ToList().Distinct().OrderBy(m => m).ToList();
e.uniprot_mods += " | ";
add = "";
foreach (var mod in ambig_mods)
{
// positions with mod
List <int> theo_ptms = ambig_id.theoretical_base.ExpandedProteinList.SelectMany(p => p
.OneBasedPossibleLocalizedModifications)
.Where(p => p.Key >= ambig_id.begin && p.Key <= ambig_id.end &&
p.Value.Select(m => UnlocalizedModification.LookUpId(m)).Contains(mod))
.Select(m => m.Key).ToList();
if (theo_ptms.Count > 0)
{
add += mod + " @ " + string.Join(", ", theo_ptms) + "; ";
}
if (ambig_id.ptm_set.ptm_combination.Where(ptm => ptm.modification.ModificationType != "Deconvolution Error" && !Proteoform.modification_is_adduct(ptm.modification)).Select(ptm => UnlocalizedModification.LookUpId(ptm.modification))
.Count(m => m == mod) > theo_ptms.Count)
{
e.novel_mods = true;
}
}
e.uniprot_mods += add;
if (add.Length == 0)
{
e.uniprot_mods += "N/A";
}
}
}
//determine level #
e.proteoform_level_description = "";
if (e.linked_proteoform_references == null)
{
e.proteoform_level = 5;
e.proteoform_level_description = "Unidentified";
}
else if (e.ambiguous_identifications.Count == 0)
{
if (e.ptm_set.ptm_combination.Count == 0)
{
e.proteoform_level = 1;
}
else
{
e.proteoform_level = 2;
e.proteoform_level_description += "PTM localization ambiguity; ";
}
//check if accessions had been grouped in constructing the theoretical database
if ((e.linked_proteoform_references.First() as TheoreticalProteoform).ExpandedProteinList.SelectMany(p => p.AccessionList).Select(a => a.Split('_')[0]).Distinct().Count() > 1)
{
e.proteoform_level += 1;
e.proteoform_level_description += "Gene ambiguity; ";
}
}
else
{
var unique_accessions = new List <string>()
{
e.linked_proteoform_references.First().accession.Split('_')[0].Split('-')[0]
}.Concat(e.ambiguous_identifications.Select(a => a.theoretical_base.accession.Split('_')[0].Split('-')[0])).Distinct();
var unique_sequences = new List <string>()
{
ExperimentalProteoform.get_sequence(e.linked_proteoform_references.First() as TheoreticalProteoform, e.begin, e.end)
}.
Concat(e.ambiguous_identifications.Select(a => ExperimentalProteoform.get_sequence(a.theoretical_base, a.begin, a.end))).Distinct();
var unique_PTMs = new List <string>()
{
string.Join(", ", e.ptm_set.ptm_combination.Where(m => m.modification.ModificationType != "Deconvolution Error").Select(ptm => UnlocalizedModification.LookUpId(ptm.modification)).OrderBy(m => m))
}.Concat(e.ambiguous_identifications.Select(a => string.Join(", ", a.ptm_set.ptm_combination.Where(m => m.modification.ModificationType != "Deconvolution Error").Select(ptm => UnlocalizedModification.LookUpId(ptm.modification))))).Distinct();
int gene_ambiguity = unique_accessions.Count() > 1 ? 1 : 0;
//check if accessions had been grouped in constructing the theoretical database
if ((e.linked_proteoform_references.First() as TheoreticalProteoform).ExpandedProteinList.SelectMany(p => p.AccessionList).Select(a => a.Split('_')[0]).Distinct().Count() > 1)
{
gene_ambiguity = 1;
}
int sequence_ambiguity = unique_sequences.Count() > 1 ? 1 : 0;
int PTM_ambiguity = unique_PTMs.Count() > 1 ? 1 : 0;
int PTM_location = e.ptm_set.ptm_combination.Count(m => m.modification.ModificationType != "Deconvolution Error") > 0 || e.ambiguous_identifications.Any(a => a.ptm_set.ptm_combination.Count(m => m.modification.ModificationType != "Deconvolution Error") > 0) ? 1 : 0;
e.proteoform_level = 1 + gene_ambiguity + sequence_ambiguity + PTM_ambiguity + PTM_location;
if (gene_ambiguity > 0)
{
e.proteoform_level_description += "Gene ambiguity; ";
}
if (sequence_ambiguity > 0)
{
e.proteoform_level_description += "Sequence ambiguity; ";
}
if (PTM_ambiguity > 0)
{
e.proteoform_level_description += "PTM identity ambiguity; ";
}
if (PTM_location > 0)
{
e.proteoform_level_description += "PTM localization ambiguity; ";
}
}
if (e.proteoform_level == 1)
{
e.proteoform_level_description = "Unambiguous";
}
//determine if new intact-mass ID
e.new_intact_mass_id = false;
if (!e.topdown_id && e.linked_proteoform_references != null && e.ambiguous_identifications.Count == 0)
{
string this_id = string.Join(",", (e.linked_proteoform_references.First() as TheoreticalProteoform).ExpandedProteinList.SelectMany(p => p.AccessionList.Select(a => a.Split('_')[0])).Distinct()) + "_" + ExperimentalProteoform.get_sequence(e.linked_proteoform_references.First() as TheoreticalProteoform, e.begin, e.end) + "_" + string.Join(", ", e.ptm_set.ptm_combination.Where(m => m.modification.ModificationType != "Deconvolution Error").Select(ptm => UnlocalizedModification.LookUpId(ptm.modification)).OrderBy(m => m));
if (!topdown_ids.Any(t => this_id.Split('_')[0].Split(',').Contains(t.Split('_')[0]) &&
this_id.Split('_')[1] == t.Split('_')[1] && this_id.Split('_')[2] == t.Split('_')[2]))
{
e.new_intact_mass_id = true;
}
}
});
if (Sweet.lollipop.remove_bad_connections)
{
if (theoretical_proteoforms.Count > 0 || (Sweet.lollipop.identify_from_td_nodes && experimental_proteoforms.Count(e => e.topdown_id) > 0))
{
Parallel.ForEach(relations, r =>
{
r.Accepted = r.Identification;
});
}
}
}
