diff --git a/mzLib/Test/TestSpectra.cs b/mzLib/Test/TestSpectra.cs
index 8a8b0eb1..450c5038 100644
--- a/mzLib/Test/TestSpectra.cs
+++ b/mzLib/Test/TestSpectra.cs
@@ -19,9 +19,13 @@
 using MassSpectrometry;
 using MzLibUtil;
 using NUnit.Framework;
+using Proteomics.PSM;
+using Readers;
 using System;
 using System.Collections.Generic;
+using System.IO;
 using System.Linq;
+using System.Text.RegularExpressions;
 using Stopwatch = System.Diagnostics.Stopwatch;
 
 namespace Test
@@ -55,6 +59,819 @@ public void Setup()
             _mzSpectrumA = new MzSpectrum(mz, intensities, false);
         }
 
+
+
+        [Test]
+        public static void MoreJunk()
+        {
+            List<string> quantResults = File.ReadAllLines(@"C:\Users\Michael Shortreed\Downloads\4-26-24 AD Brain DHAA Analysis\AllQuantifiedPeptidesMarkovich.tsv").ToList();
+            List<string> fullSequences = new List<string>();
+            foreach (var line in quantResults)
+            {
+                string[] fields = line.Split('\t');
+                fullSequences.Add(fields[0]);
+            }
+
+            string psmFilePath =
+                @"C:\Users\Michael Shortreed\Downloads\4-26-24 AD Brain DHAA Analysis\AllPeptidesMarkovich.psmtsv";
+            List<PsmFromTsv> parsedPsms = SpectrumMatchTsvReader.ReadPsmTsv(psmFilePath, out var warnings);
+
+            List<PsmFromTsv> quantPeptidesFoundInAllPeptides = new List<PsmFromTsv>();
+            foreach (var psm in parsedPsms)
+            {
+                bool containsAny = fullSequences.Any(s => psm.FullSequence.Contains(s));
+                if (containsAny)
+                {
+                    fullSequences.Remove(psm.FullSequence);
+                    quantPeptidesFoundInAllPeptides.Add(psm);
+                }
+
+                if (fullSequences.Count == 0)
+                {
+                    break;
+                }
+            }
+
+            List<string> myOut = new List<string>();
+            //myOut.Add(parsedPsms[0].ToString());
+            foreach (var psm in quantPeptidesFoundInAllPeptides)
+            {
+
+                myOut.Add(psm.ToString());
+
+            }
+
+            File.WriteAllLines(@"C:\Users\Michael Shortreed\Downloads\4-26-24 AD Brain DHAA Analysis\psmsFoundInQuantMarkovich.txt", myOut);
+
+        }
+        [Test]
+        public static void Junk3()
+        {
+
+            string psmFilePath =
+                @"C:\Users\Michael Shortreed\Downloads\4-26-24 AD Brain DHAA Analysis\AllPeptidesMarkovich.psmtsv";
+            List<PsmFromTsv> parsedPsms = SpectrumMatchTsvReader.ReadPsmTsv(psmFilePath, out var warnings);
+            parsedPsms = parsedPsms.Where(p => p.QValue < .01).ToList();
+            parsedPsms = parsedPsms.Where(p => p.DecoyContamTarget.Contains("T")).ToList();
+
+            List<string> interestingMods = new List<string> { "Y[Common Biological:Phosphorylation on Y]", "S[Common Biological:Phosphorylation on S]", "T[Common Biological:Phosphorylation on T]" };
+
+            Dictionary<(string, int), List<PsmFromTsv>> genePositionPsm = new Dictionary<(string, int), List<PsmFromTsv>>();
+
+            foreach (var psm in parsedPsms)
+            {
+                List<string> foundMods = interestingMods.Where(s => psm.FullSequence.Contains(s)).ToList();
+                if (foundMods.Any())
+                {
+                    string sequence = psm.FullSequence;
+                    foreach (var mod in foundMods)
+                    {
+                        string firstCharacter = mod.Substring(0, 1);
+                        if (firstCharacter == "Y" || firstCharacter == "S" || firstCharacter == "T")
+                        {
+                            sequence = sequence.Replace(mod, firstCharacter.ToLowerInvariant());
+                        }
+                    }
+                    sequence = Regex.Replace(sequence, "\\[(.*?)\\]", "");
+                    List<int> lowercaseLetterPositions = new List<int>();
+
+                    for (int i = 0; i < sequence.Length; i++)
+                    {
+                        if (char.IsLower(sequence[i]))
+                        {
+                            lowercaseLetterPositions.Add(i);
+                        }
+                    }
+                    string firstAndLastAminoAcidPositionInProtein = psm.StartAndEndResiduesInProtein.Split('|')[0];
+                    firstAndLastAminoAcidPositionInProtein = firstAndLastAminoAcidPositionInProtein.Substring(1, firstAndLastAminoAcidPositionInProtein.Length - 2);
+                    firstAndLastAminoAcidPositionInProtein = firstAndLastAminoAcidPositionInProtein.Replace(" to ", "\t");
+                    int[] startEnd = firstAndLastAminoAcidPositionInProtein.Split('\t').Select(int.Parse).ToArray();
+                    lowercaseLetterPositions = lowercaseLetterPositions.Select(s => s + startEnd[0]).ToList();
+
+                    string allGenesInPsm = psm.GeneName;
+                    string[] genes = allGenesInPsm.Split('|');
+                    string firstGene = genes[0].Split(':')[1];
+
+                    foreach (int position in lowercaseLetterPositions)
+                    {
+                        if (genePositionPsm.ContainsKey((firstGene, position)))
+                        {
+                            genePositionPsm[(firstGene, position)].Add(psm);
+
+                        }
+                        else
+                        {
+                            genePositionPsm.Add((firstGene, position), new List<PsmFromTsv> { psm });
+                        }
+                    }
+                }
+            }
+
+            List<string> myOut = new List<string>();
+            myOut.Add("position" + "\t" + "protein accession" + "\t" + "gene" + "\t" + "full sequence");
+
+            foreach (var kvp in genePositionPsm)
+            {
+                if (kvp.Value.Count > 1)
+                {
+                    foreach (var psm in kvp.Value)
+                    {
+                        myOut.Add(kvp.Key.Item2 + "\t" + psm.ProteinAccession + "\t" + kvp.Key.Item1 + "\t" + psm.FullSequence);
+                    }
+                }
+            }
+
+            File.WriteAllLines(@"C:\Users\Michael Shortreed\Downloads\4-26-24 AD Brain DHAA Analysis\phosphoPeptidesMarkovich.txt", myOut);
+
+        }
+
+        [Test]
+        public static void Junk4()
+        {
+            Dictionary<(string,string),string> baseSequencefullSequencQvaluePepQvalueforPSMs = new Dictionary<(string, string), string>();
+
+            using (StreamReader sr = new StreamReader(@"C:\Users\Michael Shortreed\Downloads\4-26-24 AD Brain DHAA Analysis\AllPSMsMarkovich.psmtsv"))
+            {
+                bool continueReading = true;
+                string line;
+                while ((line = sr.ReadLine()) != null && continueReading)
+                {
+                    string[] fields = line.Split('\t');
+                    string baseSequence = fields[12];
+                    string fullSequence = fields[13];
+                    string targetDecoyContam = fields[38];
+                    string qValue = fields[50];
+                    string pepQValue = fields[55];
+                    if (targetDecoyContam == "T" && double.TryParse(qValue, out double qValueDouble))
+                    {
+                        if (qValueDouble < 0.01 &&!baseSequencefullSequencQvaluePepQvalueforPSMs.ContainsKey((baseSequence,fullSequence)))
+                        {
+                            baseSequencefullSequencQvaluePepQvalueforPSMs.Add((baseSequence, fullSequence), qValue + "\t" + pepQValue);
+                        }
+
+                    }
+
+                    if (double.TryParse(qValue, out double qValueDouble2))
+                    {
+                        if (qValueDouble2 > 0.01)
+                        {
+                            continueReading = false;
+                        }
+                    }
+                }
+            }
+
+            string psmFilePath =
+                @"C:\Users\Michael Shortreed\Downloads\4-26-24 AD Brain DHAA Analysis\AllPeptidesMarkovich.psmtsv";
+            List<PsmFromTsv> parsedPeptides = SpectrumMatchTsvReader.ReadPsmTsv(psmFilePath, out var warnings);
+            parsedPeptides = parsedPeptides.Where(p => p.DecoyContamTarget.Contains("T")).ToList();
+
+            List<string> interestingMods = new List<string> { "S[Common Biological:Phosphorylation on S]", "T[Common Biological:Phosphorylation on T]", "S[Less Common:Dehydroalanine on S]", "C[Less Common:Dehydroalanine on C]",
+                "S[Custom:Homocys on S]", "C[Custom:Homocys on C]", "T[Custom:Homocys on T]", "T[Less Common:Dehydrobutyrine on T]", "S[Custom:DTT on S]", "C[Custom:DTT on C]", "C[Custom:DTT on T]", "T[Custom:Glutathione on T]", 
+                "S[Custom:Glutathione on S]", "C[Custom:Glutathione on C]", "S[Custom:TCEP on S]", "T[Custom:TCEP on T]", "C[Custom:TCEP on C]"  };
+
+            Dictionary<(string, int), List<PsmFromTsv>> genePositionPeptides = new Dictionary<(string, int), List<PsmFromTsv>>();
+            Dictionary<(string, int), List<string>> genePositionMod = new Dictionary<(string, int), List<string>>();
+            Dictionary<string,List<PsmFromTsv>> noInterestingModsPeptideValues = new Dictionary<string, List<PsmFromTsv>>();
+
+            foreach (var peptide in parsedPeptides)
+            {
+                if (baseSequencefullSequencQvaluePepQvalueforPSMs.ContainsKey((peptide.BaseSeq,peptide.FullSequence)))
+                {
+                    List<string> foundMods = interestingMods.Where(s => peptide.FullSequence.Contains(s)).ToList();
+                    if (foundMods.Any())
+                    {
+                        foreach (var mod in foundMods)
+                        {
+                            string sequence = peptide.FullSequence;
+                            string firstCharacter = mod.Substring(0, 1);
+                            if (firstCharacter == "Y" || firstCharacter == "S" || firstCharacter == "T" ||
+                                firstCharacter == "C")
+                            {
+                                sequence = sequence.Replace(mod, firstCharacter.ToLowerInvariant());
+                            }
+
+                            //eliminate the remaning mods
+                            while (sequence.Contains("[") && sequence.Contains("]"))
+                            {
+                                int firstOpenBracket = sequence.IndexOf('[');
+                                int firstCloseBracket = sequence.IndexOf(']', firstOpenBracket);
+                                if (firstCloseBracket != -1)
+                                {
+                                    sequence = sequence.Remove(firstOpenBracket, firstCloseBracket - firstOpenBracket + 1);
+                                }
+                                else
+                                {
+                                    break;
+                                }
+                            }
+
+                            List<int> lowercaseLetterPositions = new List<int>();
+
+                            for (int i = 0; i < sequence.Length; i++)
+                            {
+                                if (char.IsLower(sequence[i]))
+                                {
+                                    lowercaseLetterPositions.Add(i);
+                                }
+                            }
+
+                            string firstAndLastAminoAcidPositionInProtein =
+                                peptide.StartAndEndResiduesInProtein.Split('|')[0];
+                            firstAndLastAminoAcidPositionInProtein =
+                                firstAndLastAminoAcidPositionInProtein.Substring(1,
+                                    firstAndLastAminoAcidPositionInProtein.Length - 2);
+                            firstAndLastAminoAcidPositionInProtein =
+                                firstAndLastAminoAcidPositionInProtein.Replace(" to ", "\t");
+                            int[] startEnd = firstAndLastAminoAcidPositionInProtein.Split('\t').Select(int.Parse)
+                                .ToArray();
+                            lowercaseLetterPositions = lowercaseLetterPositions.Select(s => s + startEnd[0]).ToList();
+
+                            string allGenesInPsm = peptide.GeneName;
+                            string firstGene = "";
+                            if (allGenesInPsm.Contains("|"))
+                            {
+                                string[] genes = allGenesInPsm.Split('|');
+
+                                if (genes[0].Contains(":"))
+                                {
+                                    firstGene = genes[0].Split(':')[1];
+
+                                    foreach (int position in lowercaseLetterPositions)
+                                    {
+                                        if (genePositionPeptides.ContainsKey((firstGene, position)))
+                                        {
+                                            genePositionPeptides[(firstGene, position)].Add(peptide);
+                                            genePositionMod[(firstGene, position)]
+                                                .Add(mod + "\t" + peptide.QValue + "\t" + peptide.PEP_QValue);
+
+                                        }
+                                        else
+                                        {
+                                            genePositionPeptides.Add((firstGene, position), new List<PsmFromTsv> { peptide });
+                                            genePositionMod.Add((firstGene, position),
+                                                new List<string> { mod + "\t" + peptide.QValue + "\t" + peptide.PEP_QValue });
+                                        }
+                                    }
+                                }
+                                else
+                                {
+                                    firstGene = genes[0];
+                                    if (genes[0].Contains(":"))
+                                    {
+                                        firstGene = genes[0].Split(':')[1];
+                                    }
+                                    foreach (int position in lowercaseLetterPositions)
+                                    {
+                                        if (genePositionPeptides.ContainsKey((firstGene, position)))
+                                        {
+                                            genePositionPeptides[(firstGene, position)].Add(peptide);
+                                            genePositionMod[(firstGene, position)]
+                                                .Add(mod + "\t" + peptide.QValue + "\t" + peptide.PEP_QValue);
+
+                                        }
+                                        else
+                                        {
+                                            genePositionPeptides.Add((firstGene, position), new List<PsmFromTsv> { peptide });
+                                            genePositionMod.Add((firstGene, position),
+                                                new List<string> { mod + "\t" + peptide.QValue + "\t" + peptide.PEP_QValue });
+                                        }
+                                    }
+                                }
+                            }
+                            else
+                            {
+                                firstGene = peptide.GeneName;
+                                if (peptide.GeneName.Contains(":"))
+                                {
+                                    firstGene = peptide.GeneName.Split(':')[1];
+                                }
+
+                                foreach (int position in lowercaseLetterPositions)
+                                {
+                                    if (genePositionPeptides.ContainsKey((firstGene, position)))
+                                    {
+                                        genePositionPeptides[(firstGene, position)].Add(peptide);
+                                        genePositionMod[(firstGene, position)]
+                                            .Add(mod + "\t" + peptide.QValue + "\t" + peptide.PEP_QValue);
+
+                                    }
+                                    else
+                                    {
+                                        genePositionPeptides.Add((firstGene, position), new List<PsmFromTsv> { peptide });
+                                        genePositionMod.Add((firstGene, position),
+                                            new List<string> { mod + "\t" + peptide.QValue + "\t" + peptide.PEP_QValue });
+                                    }
+                                }
+                            }
+                        }
+                    }
+                    else
+                    {
+                        if (noInterestingModsPeptideValues.ContainsKey(peptide.BaseSeq))
+                        {
+                            noInterestingModsPeptideValues[peptide.BaseSeq].Add(peptide);
+                        }
+                        else
+                        {
+                            noInterestingModsPeptideValues.Add(peptide.BaseSeq, new List<PsmFromTsv> { peptide });
+                        }
+                        
+                    }
+                }
+            }
+
+            List<string> myOut = new List<string>();
+            myOut.Add("position" + "\t" + "protein accession" + "\t" + "gene" + "\t" + "base sequence" + "\t" + "full sequence" + "\t" + "modification" + "\t" + "Peptide Q-value" + "\t" + "Peptide PEP Q-Value" + "\t" + "PSM Q-value" + "\t" + "PSM PEP Q-Value");
+
+            foreach (var kvp in genePositionPeptides)
+            {
+                if (kvp.Value.Count > 1)
+                {
+                    foreach (var psm in kvp.Value)
+                    {
+                        int index = kvp.Value.IndexOf(psm);
+                        if(baseSequencefullSequencQvaluePepQvalueforPSMs.ContainsKey((psm.BaseSeq, psm.FullSequence)))
+                        {
+                            myOut.Add(kvp.Key.Item2 + "\t" + psm.ProteinAccession + "\t" + kvp.Key.Item1 + "\t" + psm.BaseSeq + "\t" + psm.FullSequence + "\t" + genePositionMod[kvp.Key][index] + "\t" + baseSequencefullSequencQvaluePepQvalueforPSMs[(psm.BaseSeq, psm.FullSequence)]);
+                            if (noInterestingModsPeptideValues.ContainsKey(psm.BaseSeq))
+                            {
+                                foreach (var psm2 in noInterestingModsPeptideValues[psm.BaseSeq])
+                                {
+                                    myOut.Add(kvp.Key.Item2 + "\t" + psm2.ProteinAccession + "\t" + kvp.Key.Item1 + "\t" + psm2.BaseSeq + "\t" + psm2.FullSequence + "\t" + "No Modifications of Interest" + "\t" + psm2.QValue + "\t" + psm2.PEP_QValue + "\t" + baseSequencefullSequencQvaluePepQvalueforPSMs[(psm2.BaseSeq, psm2.FullSequence)]);
+                                }
+                                noInterestingModsPeptideValues.Remove(psm.BaseSeq);
+                            }
+                        }
+                        else
+                        {
+                            myOut.Add(kvp.Key.Item2 + "\t" + psm.ProteinAccession + "\t" + kvp.Key.Item1 + "\t" + psm.BaseSeq + "\t" + psm.FullSequence + "\t" + genePositionMod[kvp.Key][index]);
+                            if (noInterestingModsPeptideValues.ContainsKey(psm.BaseSeq))
+                            {
+                                foreach (var psm2 in noInterestingModsPeptideValues[psm.BaseSeq])
+                                {
+                                    string psmQvalues = baseSequencefullSequencQvaluePepQvalueforPSMs[(psm2.BaseSeq, psm2.FullSequence)];
+                                    myOut.Add(kvp.Key.Item2 + "\t" + psm2.ProteinAccession + "\t" + kvp.Key.Item1 + "\t" + psm2.BaseSeq + "\t" + psm2.FullSequence + "\t" + "No Modifications of Interest" + "\t" + psm2.QValue + "\t" + psm2.PEP_QValue + "\t" + psmQvalues);
+                                
+                                }
+                                noInterestingModsPeptideValues.Remove(psm.BaseSeq);
+                            }
+                        }
+                        
+                    }
+                }
+            }
+
+            File.WriteAllLines(@"C:\Users\Michael Shortreed\Downloads\4-26-24 AD Brain DHAA Analysis\modPeptidesMarkovichWithPosition.txt", myOut);
+
+        }
+
+
+
+        [Test]
+        public static void Junk5()
+        {
+            List<string> interestingMods = new List<string> { "S[Common Biological:Phosphorylation on S]", "T[Common Biological:Phosphorylation on T]", "S[Less Common:Dehydroalanine on S]", "C[Less Common:Dehydroalanine on C]",
+                "S[Custom:Homocys on S]", "C[Custom:Homocys on C]", "T[Custom:Homocys on T]", "T[Less Common:Dehydrobutyrine on T]", "S[Custom:DTT on S]", "C[Custom:DTT on C]", "C[Custom:DTT on T]", "T[Custom:Glutathione on T]",
+                "S[Custom:Glutathione on S]", "C[Custom:Glutathione on C]", "S[Custom:TCEP on S]", "T[Custom:TCEP on T]", "C[Custom:TCEP on C]"  };
+
+            //string is position accession gene
+            //dictionary key is mod and int is count
+            Dictionary<string, Dictionary<string, int>> bubba = new Dictionary<string, Dictionary<string, int>>();
+            using (StreamReader sr =
+                   new StreamReader(
+                       @"C:\Users\Michael Shortreed\Downloads\4-26-24 AD Brain DHAA Analysis\modPeptidesMarkovichWithPosition.txt"))
+            {
+                bool continueReading = true;
+                string line;
+                
+                while ((line = sr.ReadLine()) != null && continueReading)
+                {
+                    
+                    string[] fields = line.Split('\t');
+                    string myKey = fields[0] + "\t" + fields[1] + "\t" + fields[2];
+
+                    bool goodLine = (double.TryParse(fields[5], out double qvalue) && qvalue < 0.01 );
+
+                    if (goodLine)
+                    {
+                        if (bubba.ContainsKey(myKey))
+                        {
+                            if (bubba[myKey].ContainsKey(fields[4]))
+                            {
+                                bubba[myKey][fields[4]]++;
+                            }
+                            else
+                            {
+                                bubba[myKey].Add(fields[4], 1);
+                            }
+                        }
+                        else
+                        {
+                            bubba.Add(myKey, new Dictionary<string, int> { { fields[4], 1 } });
+                        }
+                    }
+                }
+            }
+
+            List<string> myOut = new List<string>();
+            myOut.Add("position" + "\t" + "protein accession" + "\t" + "gene" + "\t" + String.Join('\t',interestingMods));
+
+            foreach (var kvp in bubba)
+            {
+                string myLine = kvp.Key +"\t";
+                foreach (var mod in interestingMods)
+                {
+                    if (kvp.Value.ContainsKey(mod))
+                    {
+                        myLine += kvp.Value[mod] + "\t";
+                    }
+                    else
+                    {
+                        myLine += "0\t";
+                    }
+                }
+                myOut.Add(myLine);
+            }
+
+            File.WriteAllLines(@"C:\Users\Michael Shortreed\Downloads\4-26-24 AD Brain DHAA Analysis\tableAllPeptidesMarkovich.txt", myOut);
+
+        }
+
+        [Test]
+        public static void Junk6()
+        {
+            Dictionary<(int,string,string),List<string>> modPeptidesWithPositionLines = new Dictionary<(int, string, string), List<string>>();
+            Dictionary<(int, string, string), List<string>> modPeptidesWithPositionFullSequences = new Dictionary<(int, string, string), List<string>>();
+            Dictionary<(int, string, string), List<string>> modPeptidesWithPositionBaseSequences = new Dictionary<(int, string, string), List<string>>();
+            Dictionary<string, List<string>> basePeptideToFullSequences = new Dictionary<string, List<string>>();
+
+            using (StreamReader sr =
+                   new StreamReader(
+                       @"C:\Users\Michael Shortreed\Downloads\4-26-24 AD Brain DHAA Analysis\modPeptides180WithPosition.txt"))
+            {
+                bool continueReading = true;
+                string line;
+                bool firstLine = true;
+
+                while ((line = sr.ReadLine()) != null && continueReading)
+                {
+                    if (!firstLine)
+                    {
+                        string[] fields = line.Split('\t');
+                        string myKey = fields[0] + "\t" + fields[1] + "\t" + fields[2];
+
+                        string baseSequence = fields[3];
+                        while (baseSequence.Contains("[") && baseSequence.Contains("]"))
+                        {
+                            int firstOpenBracket = baseSequence.IndexOf('[');
+                            int firstCloseBracket = baseSequence.IndexOf(']', firstOpenBracket);
+                            if (firstCloseBracket != -1)
+                            {
+                                baseSequence = baseSequence.Remove(firstOpenBracket, firstCloseBracket - firstOpenBracket + 1);
+                            }
+                            else
+                            {
+                                break;
+                            }
+                        }
+                        
+
+
+
+                        if (modPeptidesWithPositionLines.ContainsKey((int.Parse(fields[0]), fields[1], fields[2])))
+                        {
+                            modPeptidesWithPositionLines[(int.Parse(fields[0]), fields[1], fields[2])].Add(line);
+                        }
+                        else
+                        {
+                            modPeptidesWithPositionLines.Add((int.Parse(fields[0]), fields[1], fields[2]), new List<string> { line });
+                        }
+
+                        if (modPeptidesWithPositionFullSequences.ContainsKey((int.Parse(fields[0]), fields[1],
+                                fields[2])))
+                        {
+                            modPeptidesWithPositionFullSequences[(int.Parse(fields[0]), fields[1], fields[2])].Add(fields[3]);
+                        }
+                        else
+                        {
+                            modPeptidesWithPositionFullSequences.Add((int.Parse(fields[0]), fields[1], fields[2]), new List<string> { fields[3] });
+                        }
+
+                        if (modPeptidesWithPositionBaseSequences.ContainsKey((int.Parse(fields[0]), fields[1],
+                                fields[2])))
+                        {
+                            modPeptidesWithPositionBaseSequences[(int.Parse(fields[0]), fields[1], fields[2])].Add(baseSequence);
+                        }
+                        else
+                        {
+                            modPeptidesWithPositionBaseSequences.Add((int.Parse(fields[0]), fields[1], fields[2]), new List<string> { baseSequence });
+                        }
+
+                        if (basePeptideToFullSequences.ContainsKey(baseSequence))
+                        {
+                            basePeptideToFullSequences[baseSequence].Add(fields[3]);
+                        }
+                        else
+                        {
+                            basePeptideToFullSequences.Add(baseSequence, new List<string> { fields[3] });
+                        }
+                    }
+                    firstLine = false;
+                }
+            }
+
+            foreach (var kvp in modPeptidesWithPositionBaseSequences)
+            {
+                modPeptidesWithPositionBaseSequences[kvp.Key] = kvp.Value.Distinct().ToList();
+            }
+
+            foreach (var kvp in basePeptideToFullSequences)
+            {
+                basePeptideToFullSequences[kvp.Key] = kvp.Value.Distinct().ToList();
+            }
+        }
+
+        [Test]
+        public static void Junk7()
+        {
+            Dictionary<(string, string), string> baseSequencefullSequencQvaluePepQvalueforPSMs = new Dictionary<(string, string), string>();
+
+            using (StreamReader sr = new StreamReader(@"C:\Users\Michael Shortreed\Downloads\4-26-24 AD Brain DHAA Analysis\AllPSMsMarkovich.psmtsv"))
+            {
+                bool continueReading = true;
+                string line;
+                while ((line = sr.ReadLine()) != null && continueReading)
+                {
+                    string[] fields = line.Split('\t');
+                    string baseSequence = fields[12];
+                    string fullSequence = fields[13];
+                    string targetDecoyContam = fields[38];
+                    string qValue = fields[50];
+                    string pepQValue = fields[55];
+                    if (targetDecoyContam == "T" && double.TryParse(qValue, out double qValueDouble))
+                    {
+                        if (qValueDouble < 0.01 && !baseSequencefullSequencQvaluePepQvalueforPSMs.ContainsKey((baseSequence, fullSequence)))
+                        {
+                            baseSequencefullSequencQvaluePepQvalueforPSMs.Add((baseSequence, fullSequence), qValue + "\t" + pepQValue);
+                        }
+
+                    }
+
+                    if (double.TryParse(qValue, out double qValueDouble2))
+                    {
+                        if (qValueDouble2 > 0.01)
+                        {
+                            continueReading = false;
+                        }
+                    }
+                }
+            }
+
+            string psmFilePath =
+                @"C:\Users\Michael Shortreed\Downloads\4-26-24 AD Brain DHAA Analysis\AllPeptidesMarkovich.psmtsv";
+            List<PsmFromTsv> parsedPeptides = SpectrumMatchTsvReader.ReadPsmTsv(psmFilePath, out var warnings);
+            parsedPeptides = parsedPeptides.Where(p => p.DecoyContamTarget.Contains("T")).ToList();
+
+            List<string> interestingMods = new List<string> { "S[Common Biological:Phosphorylation on S]", "T[Common Biological:Phosphorylation on T]", "S[Less Common:Dehydroalanine on S]", "C[Less Common:Dehydroalanine on C]",
+                "S[Custom:Homocys on S]", "C[Custom:Homocys on C]", "T[Custom:Homocys on T]", "T[Less Common:Dehydrobutyrine on T]", "S[Custom:DTT on S]", "C[Custom:DTT on C]", "C[Custom:DTT on T]", "T[Custom:Glutathione on T]",
+                "S[Custom:Glutathione on S]", "C[Custom:Glutathione on C]", "S[Custom:TCEP on S]", "T[Custom:TCEP on T]", "C[Custom:TCEP on C]"  };
+
+            Dictionary<(string, int), List<PsmFromTsv>> genePositionPeptides = new Dictionary<(string, int), List<PsmFromTsv>>();
+            Dictionary<(string, int), List<string>> genePositionMod = new Dictionary<(string, int), List<string>>();
+            Dictionary<string, List<PsmFromTsv>> noInterestingModsPeptideValues = new Dictionary<string, List<PsmFromTsv>>();
+
+            foreach (var peptide in parsedPeptides)
+            {
+                if (baseSequencefullSequencQvaluePepQvalueforPSMs.ContainsKey((peptide.BaseSeq, peptide.FullSequence)))
+                {
+                    List<string> foundMods = interestingMods.Where(s => peptide.FullSequence.Contains(s)).ToList();
+                    if (foundMods.Any())
+                    {
+                        foreach (var mod in foundMods)
+                        {
+                            string sequence = peptide.FullSequence;
+                            string firstCharacter = mod.Substring(0, 1);
+                            if (firstCharacter == "Y" || firstCharacter == "S" || firstCharacter == "T" ||
+                                firstCharacter == "C")
+                            {
+                                sequence = sequence.Replace(mod, firstCharacter.ToLowerInvariant());
+                            }
+
+                            sequence = sequence.Replace("[I]", "");
+                            sequence = sequence.Replace("[II]", "");
+                            sequence = sequence.Replace("[III]", "");
+
+                            //eliminate the remaning mods
+                            while (sequence.Contains("[") && sequence.Contains("]"))
+                            {
+                                int firstOpenBracket = sequence.IndexOf('[');
+                                int firstCloseBracket = sequence.IndexOf(']', firstOpenBracket);
+                                if (firstCloseBracket != -1)
+                                {
+                                    sequence = sequence.Remove(firstOpenBracket, firstCloseBracket - firstOpenBracket + 1);
+                                }
+                                else
+                                {
+                                    break;
+                                }
+                            }
+
+                            List<int> lowercaseLetterPositions = new List<int>();
+
+                            for (int i = 0; i < sequence.Length; i++)
+                            {
+                                if (char.IsLower(sequence[i]))
+                                {
+                                    lowercaseLetterPositions.Add(i);
+                                }
+                            }
+
+                            string firstAndLastAminoAcidPositionInProtein =
+                                peptide.StartAndEndResiduesInProtein.Split('|')[0];
+                            firstAndLastAminoAcidPositionInProtein =
+                                firstAndLastAminoAcidPositionInProtein.Substring(1,
+                                    firstAndLastAminoAcidPositionInProtein.Length - 2);
+                            firstAndLastAminoAcidPositionInProtein =
+                                firstAndLastAminoAcidPositionInProtein.Replace(" to ", "\t");
+                            int[] startEnd = firstAndLastAminoAcidPositionInProtein.Split('\t').Select(int.Parse)
+                                .ToArray();
+                            lowercaseLetterPositions = lowercaseLetterPositions.Select(s => s + startEnd[0]).ToList();
+
+                            string allGenesInPsm = peptide.GeneName;
+                            string firstGene = "";
+                            if (allGenesInPsm.Contains("|"))
+                            {
+                                string[] genes = allGenesInPsm.Split('|');
+
+                                if (genes[0].Contains(":"))
+                                {
+                                    firstGene = genes[0].Split(':')[1];
+
+                                    foreach (int position in lowercaseLetterPositions)
+                                    {
+                                        if (genePositionPeptides.ContainsKey((firstGene, position)))
+                                        {
+                                            genePositionPeptides[(firstGene, position)].Add(peptide);
+                                            genePositionMod[(firstGene, position)]
+                                                .Add(mod + "\t" + peptide.QValue + "\t" + peptide.PEP_QValue);
+
+                                        }
+                                        else
+                                        {
+                                            genePositionPeptides.Add((firstGene, position), new List<PsmFromTsv> { peptide });
+                                            genePositionMod.Add((firstGene, position),
+                                                new List<string> { mod + "\t" + peptide.QValue + "\t" + peptide.PEP_QValue });
+                                        }
+                                    }
+                                }
+                                else
+                                {
+                                    firstGene = genes[0];
+                                    if (genes[0].Contains(":"))
+                                    {
+                                        firstGene = genes[0].Split(':')[1];
+                                    }
+                                    foreach (int position in lowercaseLetterPositions)
+                                    {
+                                        if (genePositionPeptides.ContainsKey((firstGene, position)))
+                                        {
+                                            genePositionPeptides[(firstGene, position)].Add(peptide);
+                                            genePositionMod[(firstGene, position)]
+                                                .Add(mod + "\t" + peptide.QValue + "\t" + peptide.PEP_QValue);
+
+                                        }
+                                        else
+                                        {
+                                            genePositionPeptides.Add((firstGene, position), new List<PsmFromTsv> { peptide });
+                                            genePositionMod.Add((firstGene, position),
+                                                new List<string> { mod + "\t" + peptide.QValue + "\t" + peptide.PEP_QValue });
+                                        }
+                                    }
+                                }
+                            }
+                            else
+                            {
+                                firstGene = peptide.GeneName;
+                                if (peptide.GeneName.Contains(":"))
+                                {
+                                    firstGene = peptide.GeneName.Split(':')[1];
+                                }
+
+                                foreach (int position in lowercaseLetterPositions)
+                                {
+                                    if (genePositionPeptides.ContainsKey((firstGene, position)))
+                                    {
+                                        genePositionPeptides[(firstGene, position)].Add(peptide);
+                                        genePositionMod[(firstGene, position)]
+                                            .Add(mod + "\t" + peptide.QValue + "\t" + peptide.PEP_QValue);
+
+                                    }
+                                    else
+                                    {
+                                        genePositionPeptides.Add((firstGene, position), new List<PsmFromTsv> { peptide });
+                                        genePositionMod.Add((firstGene, position),
+                                            new List<string> { mod + "\t" + peptide.QValue + "\t" + peptide.PEP_QValue });
+                                    }
+                                }
+                            }
+                        }
+                    }
+                    else
+                    {
+                        if (noInterestingModsPeptideValues.ContainsKey(peptide.BaseSeq))
+                        {
+                            noInterestingModsPeptideValues[peptide.BaseSeq].Add(peptide);
+                        }
+                        else
+                        {
+                            noInterestingModsPeptideValues.Add(peptide.BaseSeq, new List<PsmFromTsv> { peptide });
+                        }
+
+                    }
+                }
+            }
+
+            List<(string,string)> outList = new List<(string, string)>();
+            List<string> myOut = new List<string>();
+            myOut.Add("position" + "\t" + "protein accession" + "\t" + "gene" + "\t" + "base sequence" + "\t" + "full sequence" + "\t" + "modification" + "\t" + "Peptide Q-value" + "\t" + "Peptide PEP Q-Value" + "\t" + "PSM Q-value" + "\t" + "PSM PEP Q-Value");
+            
+            foreach (var kvp in genePositionPeptides)
+            {
+                if (kvp.Value.Count > 1)
+                {
+                    foreach (var psm in kvp.Value)
+                    {
+                        int index = kvp.Value.IndexOf(psm);
+                        if (baseSequencefullSequencQvaluePepQvalueforPSMs.ContainsKey((psm.BaseSeq, psm.FullSequence)))
+                        {
+                            myOut.Add(kvp.Key.Item2 + "\t" + psm.ProteinAccession + "\t" + kvp.Key.Item1 + "\t" + psm.BaseSeq + "\t" + psm.FullSequence + "\t" + genePositionMod[kvp.Key][index] + "\t" + baseSequencefullSequencQvaluePepQvalueforPSMs[(psm.BaseSeq, psm.FullSequence)]);
+                            outList.Add((psm.FullSequence, kvp.Key.Item2 + "\t" + psm.ProteinAccession + "\t" + kvp.Key.Item1 + "\t" + psm.BaseSeq + "\t" + psm.FullSequence + "\t" + genePositionMod[kvp.Key][index] + "\t" + baseSequencefullSequencQvaluePepQvalueforPSMs[(psm.BaseSeq, psm.FullSequence)]));
+                            if (noInterestingModsPeptideValues.ContainsKey(psm.BaseSeq))
+                            {
+                                foreach (var psm2 in noInterestingModsPeptideValues[psm.BaseSeq])
+                                {
+                                    myOut.Add(kvp.Key.Item2 + "\t" + psm2.ProteinAccession + "\t" + kvp.Key.Item1 + "\t" + psm2.BaseSeq + "\t" + psm2.FullSequence + "\t" + "No Modifications of Interest" + "\t" + psm2.QValue + "\t" + psm2.PEP_QValue + "\t" + baseSequencefullSequencQvaluePepQvalueforPSMs[(psm2.BaseSeq, psm2.FullSequence)]);
+                                    outList.Add((psm2.FullSequence, kvp.Key.Item2 + "\t" + psm2.ProteinAccession + "\t" + kvp.Key.Item1 + "\t" + psm2.BaseSeq + "\t" + psm2.FullSequence + "\t" + "No Modifications of Interest" + "\t" + psm2.QValue + "\t" + psm2.PEP_QValue + "\t" + baseSequencefullSequencQvaluePepQvalueforPSMs[(psm2.BaseSeq, psm2.FullSequence)]));
+                                }
+                                noInterestingModsPeptideValues.Remove(psm.BaseSeq);
+                            }
+                        }
+                        else
+                        {
+                            //myOut.Add(kvp.Key.Item2 + "\t" + psm.ProteinAccession + "\t" + kvp.Key.Item1 + "\t" + psm.BaseSeq + "\t" + psm.FullSequence + "\t" + genePositionMod[kvp.Key][index]);
+                            
+                            //if (noInterestingModsPeptideValues.ContainsKey(psm.BaseSeq))
+                            //{
+                            //    foreach (var psm2 in noInterestingModsPeptideValues[psm.BaseSeq])
+                            //    {
+                            //        string psmQvalues = baseSequencefullSequencQvaluePepQvalueforPSMs[(psm2.BaseSeq, psm2.FullSequence)];
+                            //        myOut.Add(kvp.Key.Item2 + "\t" + psm2.ProteinAccession + "\t" + kvp.Key.Item1 + "\t" + psm2.BaseSeq + "\t" + psm2.FullSequence + "\t" + "No Modifications of Interest" + "\t" + psm2.QValue + "\t" + psm2.PEP_QValue + "\t" + psmQvalues);
+
+                            //    }
+                            //    noInterestingModsPeptideValues.Remove(psm.BaseSeq);
+                            //}
+                        }
+
+                    }
+                }
+            }
+
+            Dictionary<string,string> quantDict = new Dictionary<string, string>();
+            using (StreamReader sr =
+                   new StreamReader(
+                       @"C:\Users\Michael Shortreed\Downloads\4-26-24 AD Brain DHAA Analysis\QuantifiedPeptidesNormalizedMarkovich.tsv"))
+            {
+                string line;
+                while ((line = sr.ReadLine()) != null)
+                {
+                    string[] fields = line.Split('\t');
+                    string fullSequence = fields[0];
+                    if (!quantDict.ContainsKey(fullSequence))
+                    {
+                        quantDict.Add(fullSequence, line);
+                    }
+                }
+            }
+
+            List<string> newOutList = new List<string>();
+            newOutList.Add(myOut[0] + "\t" + quantDict["Sequence"]);
+            foreach (var kvp in outList)
+            {
+                if (quantDict.ContainsKey(kvp.Item1))
+                {
+                    newOutList.Add(kvp.Item2 + "\t" + quantDict[kvp.Item1]);
+                }
+                else
+                {
+                    newOutList.Add(kvp.Item2);
+                }
+            }
+
+            File.WriteAllLines(@"C:\Users\Michael Shortreed\Downloads\4-26-24 AD Brain DHAA Analysis\modPeptidesMarkovichWithPositionAndQuant_new.txt", newOutList);
+        }
+
+
         [Test]
         public void SpectrumCount()
         {