public void Method1(double twoMinus, double a2, double y1, string y1_Ions, string a2_ions, string y1_Ions_intensity, string a2_ions_intensity)
{
status_report.Show();
populateTables();
double precursorEPD = twoMinus * 2; //No gain of H in photodetachment.
double GeneralPrecusrorDifference = precursorEPD - GeneralStructureMass; //Intact Precursor Mass - Building Block
/*The assumption with method 1 is that if there is an intense singly charged peak,
* then it is the Y1 and the y1 has no secondary chain on the 2' end on the LHS */
//CID of Y1
List <Fragment> FragmentIons_y1 = new List <Fragment>();
string[] split_ions = y1_Ions.Split(',');
string[] split_intensities = y1_Ions_intensity.Split(',');
//Do some String Parsing to get the Fragment Ions and Intensities and put them in a list for
//y1 and a2
for (int i = 0; i < split_ions.Length; i++)
{
Fragment J = new Fragment();
J.intensity = Convert.ToDouble(split_intensities[i]);
J.mass = Convert.ToDouble(split_ions[i]);
FragmentIons_y1.Add(J);
}
List <Fragment> FragmentIons_a2 = new List <Fragment>();
split_ions = a2_ions.Split(',');
split_intensities = a2_ions_intensity.Split(',');
for (int i = 0; i < split_ions.Length; i++)
{
Fragment J = new Fragment();
J.intensity = Convert.ToDouble(split_intensities[i]);
J.mass = Convert.ToDouble(split_ions[i]);
FragmentIons_a2.Add(J);
}
//Y1 time:
//Step 1: Does there exist two ions < 200 m/z from the y1? Look for doublet within 300
//Exclusively Alpha and epsilon positions for y1!!
Console.WriteLine(":::Reducing Sugar:::");
status_report.addStatusM = ":::Reducing Sugar:::";
int counter = 0;
List <Fragment> tempStorage = new List <Fragment>();
List <Fragment> non_possible_doublet = new List <Fragment>();
for (int i = 0; i < FragmentIons_y1.Count; i++)
{
if (Math.Abs(FragmentIons_y1[i].mass - y1) <= 301)
{
tempStorage.Add(FragmentIons_y1[i]);
counter++;
}
}
//Doublet is here
if (counter == 2)
{
List <Fragment> intensitySort = tempStorage.OrderBy(Fragment => Fragment.intensity).ToList();
MessageBox.Show("Frag 1: " + intensitySort[0].mass + "Frag 2: " + intensitySort[1].mass);
//3-alpha more abundant [1], 2 ep less abundant [0], we also have a 2degrees on 2'.
//3-Alpha
Console.WriteLine("The 3-Alpha on the reducing sugar is:");
status_report.addStatusM = "The 3-Alpha on the reducing sugar is:";
Double compare = Math.Abs(y1 - intensitySort[1].mass);
Console.WriteLine(primary_alpha.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key);
status_report.addStatusM = primary_alpha.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
//2-epsilon
Console.WriteLine("The 2-Epsilon on the reducing sugar is:");
status_report.addStatusM = "The 2-Epsilon on the reducing sugar is:";
compare = Math.Abs(y1 - intensitySort[0].mass);
Console.WriteLine(secondary_epsilon.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key);
status_report.addStatusM = secondary_epsilon.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
//Take the lowest mass one now! Table Value Red GLcN-OH + Acyl!
Fragment temp = FragmentIons_y1.OrderBy(Fragment => Fragment.mass).First();
//Don't need to subtract anything off. It si acyl + GlCnOH
compare = temp.mass;
Console.WriteLine("Remaining Primary 2' on Reducing Sugar is:");
status_report.addStatusM = "Remaining Primary 2' on Reducing Sugar is:";
Console.WriteLine(RedGlnOHAcyl.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key);
status_report.addStatusM = RedGlnOHAcyl.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
}
//Something went wrong
else if (counter >= 2)
{
MessageBox.Show("Error! Found > 2 ions when searching for doublets");
}
//There is no doublet, different analysis.
else
{
//Come back with an example here later - WRP
Console.WriteLine("Either two primary chains or a 2' chain wtih secondary and OH. Ambigous Structure results.");
status_report.addStatusM = "Either two primary chains or a 2' chain wtih secondary and OH. Ambigous Structure results.";
}
//Characterize the A2, we already know that there is no secondary chain on the 2'
Console.WriteLine(":::NonReducing Sugar:::");
status_report.addStatusM = ":::NonReducing Sugar:::";
double theoretical_a2 = (precursorEPD - y1) + 60;
if (Math.Abs(theoretical_a2 - a2) >= 2)
{
MessageBox.Show("Theroretical a2 ion is " + theoretical_a2 + " and input a2 ion is " + a2 + " Will continue running, but please ensure values are correct!", "Warning!");
}
//You always get 3B and 3alpha here! always, 3beta > 3alpha NL result ions, so 3beta is last element, use it.
List <Fragment> intensitySort2 = FragmentIons_a2.OrderBy(Fragment => Fragment.mass).ToList();
if (intensitySort2.Count == 2)
{
if (Math.Abs(intensitySort2[0].mass - intensitySort2[1].mass) <= 20)
{
Console.WriteLine("Doublets only, meaning that 3 is primary on nonreducing sugar");
status_report.addStatusM = "Doublets only, meaning that 3' is primary on nonreducing sugar";
Double compare = Math.Abs(a2 - intensitySort2[1].mass);
Console.WriteLine(primary_beta.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key);
status_report.addStatusM = primary_beta.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
Console.WriteLine("2 Sugar is");
status_report.addStatusM = "2 Sugar is";
compare = intensitySort2[1].mass;
Console.WriteLine(NRGlnOHAcyl.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key);
status_report.addStatusM = NRGlnOHAcyl.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
}
//Secondary Chain exists otherwise on 2' end.
else
{
//The epsilon is the mmost dominant. First NL.
//The lowest mass is the loss of both acyl chains, more abundant is the loss of epsilon side chain.
Console.WriteLine("Two Neutral losses. 3 sugar has 2 chains");
status_report.addStatusM = "Two Neutral losses. 3 sugar has 2 chains";
Console.WriteLine("Secondary Chain on 3 end:");
status_report.addStatusM = "Secondary Chain on 3 end:";
Double compare = Math.Abs(a2 - intensitySort2[1].mass);
Console.WriteLine(secondary_epsilon.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key);
status_report.addStatusM = secondary_epsilon.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
Console.WriteLine("Primary Chain on 3 end:");
status_report.addStatusM = "Primary Chain on 3 end:";
compare = Math.Abs(intensitySort2[1].mass - intensitySort2[0].mass);
//This is beta cleavage.
Console.WriteLine(primary_beta.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key);
status_report.addStatusM = primary_beta.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
Console.WriteLine("2 End:");
status_report.addStatusM = "2 End:";
compare = intensitySort2[0].mass;
Console.WriteLine(NRGlnOHAcyl.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key);
status_report.addStatusM = NRGlnOHAcyl.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
}
}
else if (intensitySort2.Count < 2)
{
Console.WriteLine("3 on Nonreducing sugar is OH");
status_report.addStatusM = "3 on Nonreducing sugar is OH";
}
else if (intensitySort2.Count > 3)
{
//NEED 3 epsilon here!
Console.WriteLine("Not Possible > 3 acyl chains. Do not include alpha cleavage if very low abundance");
status_report.addStatusM = "Not Possible > 3 acyl chains. Do not include alpha cleavage if very low abundance";
}
}
public void Method2(double twoMinus, double a2, double y1, string y1_Ions, string a2_ions, string y1_Ions_intensity, string a2_ions_intensity, double x1, double x1plus52, double Precursor2)
{
Boolean primary_nonred_3 = false;
populateTables();
status_report.Show();
Console.WriteLine("Performing Method 2");
status_report.addStatusM = "Performing Method 2";
//We need to know the second precursor chosen, as that particular ion will give us an important NL
Double compare = Math.Abs(twoMinus - Precursor2) * 2;
TableElement test1 = secondary_epsilon.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First();
TableElement test2 = primary_beta.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First();
//We need to figure out which of these is actualyl corresponding to the 3' cleavage from the NL.
if (Math.Abs(compare - test1.Value) < Math.Abs(compare - test2.Value))
{
Console.WriteLine("1st Neutral Loss: The 3-epsilon cleavage of the Non-Reducing Sugar is:");
status_report.addStatusM = "1st Neutral Loss: The 3-epsilon cleavage of the Non-Reducing Sugar is:";
Console.WriteLine(test1.Key);
status_report.addStatusM = test1.Key;
primary_nonred_3 = false;
}
else
{
Console.WriteLine("1st Neutral Loss: The 3-beta cleavage of the Non-Reducing Sugar is:");
status_report.addStatusM = "1st Neutral Loss: The 3-beta cleavage of the Non-Reducing Sugar is:";
Console.WriteLine(test2.Key);
status_report.addStatusM = test2.Key;
primary_nonred_3 = true;
}
// status_report.addStatusM = secondary_epsilon.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
//Make sure Y1 and X1 agree..
if (Math.Abs(x1 - y1) > 30 || Math.Abs(x1 - y1) < 27 || x1 < y1)
{
Microsoft.VisualBasic.Interaction.MsgBox("Warning! X1 should be > y1 and they should be approximately 28 Da between each other. Please check your values.");
}
//Y1 Analysis is the same.....
double precursorEPD = twoMinus * 2; //No gain of H in photodetachment.
double GeneralPrecusrorDifference = precursorEPD - GeneralStructureMass; //Intact Precursor Mass - Building Block
/*The assumption with method 1 is that if there is an intense singly charged peak,
* then it is the Y1 and the y1 has no secondary chain on the 2' end on the LHS */
//CID of Y1
List <Fragment> FragmentIons_y1 = new List <Fragment>();
string[] split_ions = y1_Ions.Split(',');
string[] split_intensities = y1_Ions_intensity.Split(',');
//Do some String Parsing to get the Fragment Ions and Intensities and put them in a list for
//y1 and a2
for (int i = 0; i < split_ions.Length; i++)
{
Fragment J = new Fragment();
J.intensity = Convert.ToDouble(split_intensities[i]);
J.mass = Convert.ToDouble(split_ions[i]);
FragmentIons_y1.Add(J);
}
List <Fragment> FragmentIons_a2 = new List <Fragment>();
split_ions = a2_ions.Split(',');
split_intensities = a2_ions_intensity.Split(',');
for (int i = 0; i < split_ions.Length; i++)
{
Fragment J = new Fragment();
J.intensity = Convert.ToDouble(split_intensities[i]);
J.mass = Convert.ToDouble(split_ions[i]);
FragmentIons_a2.Add(J);
}
//Y1 Analysis:
//Step 1: Does there exist two ions < 200 m/z from the y1? Look for doublet within 300
//Exclusively Alpha and epsilon positions for y1
Console.WriteLine(":::Reducing Sugar:::");
status_report.addStatusM = ":::Reducing Sugar:::";
int counter = 0;
List <Fragment> tempStorage = new List <Fragment>();
List <Fragment> non_possible_doublet = new List <Fragment>();
for (int i = 0; i < FragmentIons_y1.Count; i++)
{
if (Math.Abs(FragmentIons_y1[i].mass - y1) <= 301)
{
tempStorage.Add(FragmentIons_y1[i]);
counter++;
}
}
//Doublet is here
if (counter == 2)
{
List <Fragment> intensitySort = tempStorage.OrderBy(Fragment => Fragment.intensity).ToList();
//3-alpha more abundant [1], 2 ep less abundant [0], we also have a 2degrees on 2'.
//3-Alpha
Console.WriteLine("The 3-Alpha on the reducing sugar is:");
status_report.addStatusM = "The 3-Alpha on the reducing sugar is:";
compare = Math.Abs(y1 - intensitySort[1].mass);
Console.WriteLine(primary_alpha.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key);
status_report.addStatusM = primary_alpha.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
//2-epsilon
Console.WriteLine("The 2-Epsilon on the reducing sugar is:");
status_report.addStatusM = "The 2-Epsilon on the reducing sugar is:";
compare = Math.Abs(y1 - intensitySort[0].mass);
Console.WriteLine(secondary_epsilon.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key);
status_report.addStatusM = secondary_epsilon.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
//Take the lowest mass one now! Table Value Red GLcN-OH + Acyl!
Fragment temp = FragmentIons_y1.OrderBy(Fragment => Fragment.mass).First();
//Don't need to subtract anything off. It si acyl + GlCnOH
compare = temp.mass;
Console.WriteLine("Remaining Primary 2' on Reducing Sugar is:");
status_report.addStatusM = "Remaining Primary 2' on Reducing Sugar is:";
Console.WriteLine(RedGlnOHAcyl.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key);
status_report.addStatusM = RedGlnOHAcyl.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
}
//Something went wrong
else if (counter >= 2)
{
MessageBox.Show("Error! Found > 2 ions when searching for doublets");
}
//There is no doublet, different analysis.
else
{
//Come back with an example here later - WRP
Console.WriteLine("Either two primary chains or a 2' chain wtih secondary and OH. Ambigous Structure results.");
status_report.addStatusM = "Either two primary chains or a 2' chain wtih secondary and OH. Ambigous Structure results.";
}
//A2 Analysis -- There are only a couple of cases. 1. 3' end is primary, and is not included in truncated a2 1 peak, 2'-epsilon or
//the 3' is secondary, and we have a primary chain left on truncated chain (3 peaks, alpha, beta, and 2'-Epsilon.
//Alpha and beta are always higher in intensity than epsilon loss.
Console.WriteLine(":::NonReducing Sugar:::");
status_report.addStatusM = ":::NonReducing Sugar:::";
double theoretical_a2 = (precursorEPD - y1) + 60; //Untruncated
List <Fragment> intensitySort2 = FragmentIons_a2.OrderBy(Fragment => Fragment.intensity).ToList();
Double beta_loss = 0;
if (primary_nonred_3 == false)
{
Console.WriteLine("The 3 end has a secondary chain on NR sugar");
status_report.addStatusM = "The 3 end has a secondary chain on NR sugar";
//This should always be true.
if (intensitySort2.Count == 3)
{
if (Math.Abs(intensitySort2[1].mass - intensitySort2[2].mass) <= 30)
{
Console.WriteLine("Doublet Found!");
status_report.addStatusM = "Doublet found!";
if (intensitySort2[1].mass > intensitySort2[2].mass)
{
beta_loss = intensitySort2[1].mass;
Console.WriteLine(intensitySort2[1].mass + "Is the beta cleavage");
status_report.addStatusM = "The 3 chain on the NR sugar is:";
compare = Math.Abs(a2 - intensitySort2[1].mass);
Console.WriteLine(primary_beta.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key);
status_report.addStatusM = primary_beta.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
}
else
{
beta_loss = intensitySort2[2].mass;
Console.WriteLine(intensitySort2[2].mass + "Is the beta cleavage");
compare = Math.Abs(a2 - intensitySort2[2].mass);
status_report.addStatusM = "The 3 chain on the NR sugar is:";
Console.WriteLine(primary_beta.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key);
status_report.addStatusM = primary_beta.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
}
status_report.addStatusM = "The 2 secondary acyl chain is:";
compare = Math.Abs(a2 - intensitySort2[0].mass);
status_report.addStatusM = secondary_epsilon.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
status_report.addStatusM = "The remaining (primary) 2 acyl chain is:";
compare = Math.Abs(beta_loss - Math.Abs(intensitySort2[0].mass - a2));
status_report.addStatusM = NRGlnOHAcyl.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
}
else
{
status_report.addStatusM = "ERR: There should be a doublet detected less ~28 Da apart.";
}
}
else
{
status_report.addStatusM = "ERR: There should be 3 ions corresponding to neutral losses: 3-alpha, 3-beta, and 2-epsilon";
}
}
//SHould only be one peak
else
{
if (intensitySort2.Count != 1)
{
status_report.addStatusM = "Should be only 1 ion!";
}
//Do Analysis.
else
{
status_report.addStatusM = "The 2 secondary acyl chain is:";
compare = Math.Abs(a2 - intensitySort2[0].mass);
status_report.addStatusM = secondary_epsilon.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
status_report.addStatusM = "The remaining (primary) 2 acyl chain is:";
compare = intensitySort2[0].mass;
status_report.addStatusM = NRGlnOHAcyl.OrderBy(TableElement => Math.Abs(compare - TableElement.Value)).First().Key;
}
}
if (intensitySort2.Count > 3)
{
Console.WriteLine("Not Possible > 3 acyl chains. Do not include alpha cleavage if very low abundance");
status_report.addStatusM = "Not Possible > 3 acyl chains. Do not include alpha cleavage if very low abundance";
}
//End A2
//The presence of an x1+52 implies that there is no acyl chain of the 3'C of the non reducing sugar! Not really needed.
// Reverification!
if (x1plus52 == -1)
{
Console.WriteLine("No X1+52, There should be no secondary acyl chain on the 3'C of the non reducing sugar.");
status_report.addStatusM = "No X1+52, There should be no secondary acyl chain on the 3'C of the non reducing sugar.";
}
else
{
Console.WriteLine("X1+52 present, There should be a secondary acyl chain on the 3'C of the non reducing sugar.");
status_report.addStatusM = "X1+52 present, There should be a secondary acyl chain on the 3'C of the non reducing";
}
//
}
