diff --git a/ProteoformSuiteGUI/DisplayObjects/DisplayGoTermNumber.cs b/ProteoformSuiteGUI/DisplayObjects/DisplayGoTermNumber.cs
index e270ef4f..b1bc9c75 100644
--- a/ProteoformSuiteGUI/DisplayObjects/DisplayGoTermNumber.cs
+++ b/ProteoformSuiteGUI/DisplayObjects/DisplayGoTermNumber.cs
@@ -10,6 +10,7 @@ namespace ProteoformSuiteGUI
 {
     public class DisplayGoTermNumber : DisplayObject
     {
+
         #region Public Constructors
 
         public DisplayGoTermNumber(GoTermNumber g)
@@ -48,7 +49,7 @@ public string ID
 
         public double p_value
         {
-            get { return gtn.by; }
+            get { return gtn.p_value; }
         }
 
         public double by //benjamini yekutieli calculated after all p-values are calculated
@@ -138,5 +139,6 @@ private static string number_format(string property_name)
         }
 
         #endregion Private Methods
+
     }
 }
diff --git a/ProteoformSuiteGUI/DisplayUtility.cs b/ProteoformSuiteGUI/DisplayUtility.cs
index 26de9c93..194b9e31 100644
--- a/ProteoformSuiteGUI/DisplayUtility.cs
+++ b/ProteoformSuiteGUI/DisplayUtility.cs
@@ -197,6 +197,16 @@ public static DataTable FormatTable(List<DisplayObject> display_objects, IEnumer
             return dt;
         }
 
+        public static bool CheckForProteinFastas(ComboBox cmb, IEnumerable<string> files)
+        {
+            if (Lollipop.file_filters[cmb.SelectedIndex].Contains(".fasta") && files.Any(x => x.Contains(".fasta")))
+            {
+                MessageBox.Show("Usage of protein fasta files is not yet enabled. Please use a protein XML file for now, e.g. from UniProt. (See this site for more information, and let us know there if this is an issue for you: https://github.com/smith-chem-wisc/ProteoformSuite/issues/477.)", "Load Files Message");
+                return true;
+            }
+            return false;
+        }
+
         #endregion Public Methods
 
     }
diff --git a/ProteoformSuiteGUI/LoadDeconvolutionResults.cs b/ProteoformSuiteGUI/LoadDeconvolutionResults.cs
index c79b54e2..e49a36e5 100644
--- a/ProteoformSuiteGUI/LoadDeconvolutionResults.cs
+++ b/ProteoformSuiteGUI/LoadDeconvolutionResults.cs
@@ -205,6 +205,7 @@ private void dgv_quantResults_DragEnter(object sender, DragEventArgs e)
         private void drag_drop(DragEventArgs e, ComboBox cmb, DataGridView dgv)
         {
             string[] files = (string[])e.Data.GetData(DataFormats.FileDrop);
+            if (DisplayUtility.CheckForProteinFastas(cmb, files)) return; // todo: implement protein fasta usage
             Sweet.lollipop.enter_input_files(files, Lollipop.acceptable_extensions[cmb.SelectedIndex], Lollipop.file_types[cmb.SelectedIndex], Sweet.lollipop.input_files, true);
             match_files();
             DisplayUtility.FillDataGridView(dgv, Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[cmb.SelectedIndex]).Select(f => new DisplayInputFile(f)));
@@ -295,6 +296,7 @@ private void add_files(ComboBox cmb, DataGridView dgv)
             DialogResult dr = openFileDialog.ShowDialog();
             if (dr == DialogResult.OK)
             {
+                if (DisplayUtility.CheckForProteinFastas(cmb, openFileDialog.FileNames)) return; // todo: implement protein fasta usage
                 Sweet.lollipop.enter_input_files(openFileDialog.FileNames, Lollipop.acceptable_extensions[cmb.SelectedIndex], Lollipop.file_types[cmb.SelectedIndex], Sweet.lollipop.input_files, true);
                 match_files();
             }
diff --git a/ProteoformSuiteGUI/ProteoformFamilies.cs b/ProteoformSuiteGUI/ProteoformFamilies.cs
index 905c7c3c..b38465d2 100644
--- a/ProteoformSuiteGUI/ProteoformFamilies.cs
+++ b/ProteoformSuiteGUI/ProteoformFamilies.cs
@@ -16,6 +16,23 @@ public partial class ProteoformFamilies : Form, ISweetForm
         public ProteoformFamilies()
         {
             InitializeComponent();
+
+            //Initialize display options
+            cmbx_colorScheme.Items.AddRange(CytoscapeScript.color_scheme_names);
+            cmbx_nodeLayout.Items.AddRange(Lollipop.node_positioning);
+            cmbx_nodeLabelPositioning.Items.AddRange(CytoscapeScript.node_label_positions);
+            cmbx_edgeLabel.Items.AddRange(Lollipop.edge_labels);
+            cmbx_nodeLabel.Items.AddRange(Lollipop.node_labels);
+            cmbx_geneLabel.Items.AddRange(Lollipop.gene_name_labels.ToArray());
+            cmbx_tableSelector.Items.AddRange(table_names);
+
+            cmbx_colorScheme.SelectedIndex = 1;
+            cmbx_nodeLayout.SelectedIndex = 1;
+            cmbx_nodeLabelPositioning.SelectedIndex = 0;
+            cmbx_edgeLabel.SelectedIndex = 1;
+            cmbx_nodeLabel.SelectedIndex = 1;
+            cmbx_geneLabel.SelectedIndex = 1;
+
             InitializeParameterSet();
             this.AutoScroll = true;
             this.AutoScrollMinSize = this.ClientSize;
@@ -43,21 +60,6 @@ public void initialize_every_time()
 
         public void InitializeParameterSet()
         {
-            //Initialize display options
-            cmbx_colorScheme.Items.AddRange(CytoscapeScript.color_scheme_names);
-            cmbx_nodeLayout.Items.AddRange(Lollipop.node_positioning);
-            cmbx_nodeLabelPositioning.Items.AddRange(CytoscapeScript.node_label_positions);
-            cmbx_edgeLabel.Items.AddRange(Lollipop.edge_labels);
-            cmbx_nodeLabel.Items.AddRange(Lollipop.node_labels);
-            cmbx_geneLabel.Items.AddRange(Lollipop.gene_name_labels.ToArray());
-            cmbx_tableSelector.Items.AddRange(table_names);
-
-            cmbx_colorScheme.SelectedIndex = 1;
-            cmbx_nodeLayout.SelectedIndex = 1;
-            cmbx_nodeLabelPositioning.SelectedIndex = 0;
-            cmbx_edgeLabel.SelectedIndex = 1;
-            cmbx_nodeLabel.SelectedIndex = 1;
-            cmbx_geneLabel.SelectedIndex = 1;
             Lollipop.preferred_gene_label = cmbx_geneLabel.SelectedItem.ToString();
             Lollipop.gene_centric_families = cb_geneCentric.Checked;
 
@@ -123,22 +125,17 @@ public void ClearListsTablesFigures(bool clear_following)
             }
         }
 
+        /// <summary>
+        /// generate report and change selected table names based on # decoy communities
+        /// </summary>
         public void update_figures_of_merit()
         {
             rtb_proteoformFamilyResults.Text = ResultsSummaryGenerator.proteoform_families_report();
-
-            //change selected table names based on # decoy communities
-            int decoy_communities = Sweet.lollipop.decoy_proteoform_communities.Count;
-            for(int i = 0; i < decoy_communities; i++)
-            {
-               if (!cmbx_tableSelector.Items.Contains("Decoy Community " + i)) cmbx_tableSelector.Items.Add("Decoy Community " + i);
-            }
-
-            //if more items than decoy databases, remove later ones //FIX   
-            while(cmbx_tableSelector.Items.Count - 5 - decoy_communities > 0)
-            {
-                cmbx_tableSelector.Items.RemoveAt(5 + decoy_communities);
-            }
+            int selection = cmbx_tableSelector.SelectedIndex;
+            cmbx_tableSelector.Items.Clear();
+            cmbx_tableSelector.Items.AddRange(table_names);
+            cmbx_tableSelector.Items.AddRange(Enumerable.Range(0, Sweet.lollipop.decoy_proteoform_communities.Count).Select(i => "Decoy Community " + i).ToArray());
+            cmbx_tableSelector.SelectedIndex = selection < cmbx_tableSelector.Items.Count ? selection : 0;
         }
 
         #endregion Public Methods
diff --git a/ProteoformSuiteGUI/ProteoformSweet.cs b/ProteoformSuiteGUI/ProteoformSweet.cs
index 21287d03..da28bbf2 100644
--- a/ProteoformSuiteGUI/ProteoformSweet.cs
+++ b/ProteoformSuiteGUI/ProteoformSweet.cs
@@ -210,7 +210,7 @@ private bool load_method()
                 string method_filename = methodFileOpen.FileName;
                 DialogResult d4 = MessageBox.Show("Add files at the listed paths if they still exist?", "Full Run", MessageBoxButtons.YesNoCancel);
                 if (d4 == DialogResult.Cancel) return false;
-                if (!open_method(File.ReadAllLines(method_filename), d4 == DialogResult.Yes))
+                if (!open_method(method_filename, File.ReadAllLines(method_filename), d4 == DialogResult.Yes))
                 {
                     MessageBox.Show("Method file was not loaded succesffully.");
                     return false;
@@ -223,9 +223,9 @@ private bool load_method()
             return false;
         }
 
-        public bool open_method(string[] lines, bool add_files)
+        public bool open_method(string methodFilePath, string[] lines, bool add_files)
         {
-            bool method_file_success = Sweet.open_method(String.Join(Environment.NewLine, lines), add_files, out string warning);
+            bool method_file_success = Sweet.open_method(methodFilePath, String.Join(Environment.NewLine, lines), add_files, out string warning);
             if (warning.Length > 0 && MessageBox.Show("WARNING" + Environment.NewLine + Environment.NewLine + warning, "Open Method", MessageBoxButtons.OKCancel) == DialogResult.Cancel)
                 return false;
             foreach (ISweetForm form in forms) form.InitializeParameterSet();
@@ -246,7 +246,7 @@ public Stopwatch full_run()
                     DialogResult d4 = MessageBox.Show("Add files at the listed paths if they still exist?", "Full Run", MessageBoxButtons.YesNoCancel);
                     if (d4 == DialogResult.Cancel) return null;
 
-                    if (!open_method(File.ReadAllLines(filepath), d4 == DialogResult.Yes))
+                    if (!open_method(filepath, File.ReadAllLines(filepath), d4 == DialogResult.Yes))
                     {
                         MessageBox.Show("Error in method file. Generate a new method file.");
                         return null;
diff --git a/ProteoformSuiteGUI/Quantification.cs b/ProteoformSuiteGUI/Quantification.cs
index c9fb1676..9d822b3e 100755
--- a/ProteoformSuiteGUI/Quantification.cs
+++ b/ProteoformSuiteGUI/Quantification.cs
@@ -20,6 +20,25 @@ public Quantification()
             InitializeComponent();
             this.AutoScroll = true;
             this.AutoScrollMinSize = this.ClientSize;
+
+            //Initialize display options
+            cmbx_volcanoChartSelection.Items.AddRange(volcano_selections);
+            cmbx_colorScheme.Items.AddRange(CytoscapeScript.color_scheme_names);
+            cmbx_nodeLayout.Items.AddRange(Lollipop.node_positioning);
+            cmbx_nodeLabelPositioning.Items.AddRange(CytoscapeScript.node_label_positions);
+            cmbx_edgeLabel.Items.AddRange(Lollipop.edge_labels.ToArray());
+            cmbx_nodeLabel.Items.AddRange(Lollipop.node_labels.ToArray());
+            cmbx_geneLabel.Items.AddRange(Lollipop.gene_name_labels.ToArray());
+            cb_redBorder.Checked = true;
+            cb_boldLabel.Checked = true;
+
+            cmbx_volcanoChartSelection.SelectedIndex = 0;
+            cmbx_colorScheme.SelectedIndex = 1;
+            cmbx_nodeLayout.SelectedIndex = 1;
+            cmbx_nodeLabelPositioning.SelectedIndex = 0;
+            cmbx_geneLabel.SelectedIndex = 1;
+            cmbx_nodeLabel.SelectedIndex = 1;
+            cmbx_edgeLabel.SelectedIndex = 1;
         }
 
         #endregion Constructor
@@ -201,29 +220,10 @@ public void InitializeConditionsParameters()
             Sweet.lollipop.numerator_condition = cmbx_ratioNumerator.SelectedItem.ToString();
             Sweet.lollipop.denominator_condition = cmbx_ratioDenominator.SelectedItem.ToString();
             Sweet.lollipop.induced_condition = cmbx_inducedCondition.SelectedItem.ToString();
-            cmbx_edgeLabel.Items.AddRange(Lollipop.edge_labels);
         }
 
         public void InitializeParameterSet()
         {
-            //Initialize display options
-            cmbx_volcanoChartSelection.Items.AddRange(volcano_selections);
-            cmbx_colorScheme.Items.AddRange(CytoscapeScript.color_scheme_names);
-            cmbx_nodeLayout.Items.AddRange(Lollipop.node_positioning);
-            cmbx_nodeLabelPositioning.Items.AddRange(CytoscapeScript.node_label_positions);
-            cmbx_edgeLabel.Items.AddRange(Lollipop.edge_labels.ToArray());
-            cmbx_nodeLabel.Items.AddRange(Lollipop.node_labels.ToArray());
-            cmbx_geneLabel.Items.AddRange(Lollipop.gene_name_labels.ToArray());
-            cb_redBorder.Checked = true;
-            cb_boldLabel.Checked = true;
-
-            cmbx_volcanoChartSelection.SelectedIndex = 0;
-            cmbx_colorScheme.SelectedIndex = 1;
-            cmbx_nodeLayout.SelectedIndex = 1;
-            cmbx_nodeLabelPositioning.SelectedIndex = 0;
-            cmbx_geneLabel.SelectedIndex = 1;
-            cmbx_nodeLabel.SelectedIndex = 1;
-            cmbx_edgeLabel.SelectedIndex = 1;
             Lollipop.preferred_gene_label = cmbx_geneLabel.SelectedItem.ToString();
             Lollipop.gene_centric_families = cb_geneCentric.Checked;
 
diff --git a/ProteoformSuiteGUI/TheoreticalDatabase.cs b/ProteoformSuiteGUI/TheoreticalDatabase.cs
index 0243c808..bc3ea62a 100644
--- a/ProteoformSuiteGUI/TheoreticalDatabase.cs
+++ b/ProteoformSuiteGUI/TheoreticalDatabase.cs
@@ -45,11 +45,12 @@ private void TheoreticalDatabase_Load(object sender, EventArgs e)
             initial_load = false;
         }
 
-        private void set_Make_Database_Button()
+        private bool SetMakeDatabaseButton()
         {
             bool ready_to_run = ReadyToRunTheGamut();
             btn_downloadUniProtPtmList.Enabled = !ready_to_run && Sweet.lollipop.get_files(Sweet.lollipop.input_files, Purpose.PtmList).Count() == 0;
             btn_Make_Databases.Enabled = ready_to_run;
+            return ready_to_run;
         }
 
         private void btn_Make_Databases_Click(object sender, EventArgs e)
@@ -278,7 +279,10 @@ private void cb_limitLargePtmSets_CheckedChanged(object sender, EventArgs e)
         private void dgv_loadFiles_DragDrop(object sender, DragEventArgs e)
         {
             drag_drop(e, cmb_loadTable, dgv_loadFiles);
-            set_Make_Database_Button();
+            if (!SetMakeDatabaseButton() && Sweet.lollipop.get_files(Sweet.lollipop.input_files, Purpose.ProteinDatabase).Count() > 0)
+            {
+                MessageBox.Show("You still need a PTM list. Please use the \"Donwload UniProt PTM List\" button.", "Enabling Make Database Button");
+            }
         }
 
         private void dgv_loadFiles_DragEnter(object sender, DragEventArgs e)
@@ -289,6 +293,7 @@ private void dgv_loadFiles_DragEnter(object sender, DragEventArgs e)
         private void drag_drop(DragEventArgs e, ComboBox cmb, DataGridView dgv)
         {
             string[] files = (string[])e.Data.GetData(DataFormats.FileDrop);
+            if (DisplayUtility.CheckForProteinFastas(cmb, files)) return; // todo: implement protein fasta usage
             Sweet.lollipop.enter_input_files(files, Lollipop.acceptable_extensions[cmb.SelectedIndex], Lollipop.file_types[cmb.SelectedIndex], Sweet.lollipop.input_files, true);
             DisplayUtility.FillDataGridView(dgv, Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[cmb.SelectedIndex]).Select(f => new DisplayInputFile(f)));
             DisplayInputFile.FormatInputFileTable(dgv, Lollipop.file_types[cmb.SelectedIndex]);
@@ -302,7 +307,10 @@ public void reload_database_list()
             DisplayUtility.FillDataGridView(dgv_loadFiles, Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[cmb_loadTable.SelectedIndex]).Select(f => new DisplayInputFile(f)));
             DisplayInputFile.FormatInputFileTable(dgv_loadFiles, Lollipop.file_types[cmb_loadTable.SelectedIndex]);
             initialize_table_bindinglist();
-            set_Make_Database_Button();
+            if (!SetMakeDatabaseButton() && Sweet.lollipop.get_files(Sweet.lollipop.input_files, Purpose.ProteinDatabase).Count() > 0)
+            {
+                MessageBox.Show("You still need a PTM list. Please use the \"Donwload UniProt PTM List\" button.", "Enabling Make Database Button");
+            }
         }
 
         private void tb_tableFilter_TextChanged(object sender, EventArgs e)
@@ -326,6 +334,7 @@ private void btn_downloadUniProtPtmList_Click(object sender, EventArgs e)
             DisplayUtility.FillDataGridView(dgv_loadFiles, Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[cmb_loadTable.SelectedIndex]).Select(f => new DisplayInputFile(f)));
             DisplayInputFile.FormatInputFileTable(dgv_loadFiles, Lollipop.file_types[cmb_loadTable.SelectedIndex]);
             btn_downloadUniProtPtmList.Enabled = false;
+            SetMakeDatabaseButton();
         }
 
         #endregion LOAD DATABASES GRID VIEW Private Methods
@@ -341,11 +350,17 @@ private void btn_addFiles_Click(object sender, EventArgs e)
 
             DialogResult dr = openFileDialog.ShowDialog();
             if (dr == DialogResult.OK)
+            {
+                if (DisplayUtility.CheckForProteinFastas(cmb_loadTable, openFileDialog.FileNames)) return; // todo: implement protein fasta usage
                 Sweet.lollipop.enter_input_files(openFileDialog.FileNames, Lollipop.acceptable_extensions[cmb_loadTable.SelectedIndex], Lollipop.file_types[cmb_loadTable.SelectedIndex], Sweet.lollipop.input_files, true);
+            }
 
             DisplayUtility.FillDataGridView(dgv_loadFiles, Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[cmb_loadTable.SelectedIndex]).Select(f => new DisplayInputFile(f)));
             DisplayInputFile.FormatInputFileTable(dgv_loadFiles, Lollipop.file_types[cmb_loadTable.SelectedIndex]);
-            set_Make_Database_Button();
+            if (!SetMakeDatabaseButton() && Sweet.lollipop.get_files(Sweet.lollipop.input_files, Purpose.ProteinDatabase).Count() > 0)
+            {
+                MessageBox.Show("You still need a PTM list. Please use the \"Donwload UniProt PTM List\" button.", "Enabling Make Database Button");
+            }
         }
 
         private void btn_clearFiles_Click(object sender, EventArgs e)
@@ -355,7 +370,7 @@ private void btn_clearFiles_Click(object sender, EventArgs e)
             Sweet.lollipop.input_files = Sweet.lollipop.input_files.Except(files_to_remove).ToList();
             DisplayUtility.FillDataGridView(dgv_loadFiles, Sweet.lollipop.get_files(Sweet.lollipop.input_files, Lollipop.file_types[cmb_loadTable.SelectedIndex]).Select(f => new DisplayInputFile(f)));
             DisplayInputFile.FormatInputFileTable(dgv_loadFiles, Lollipop.file_types[cmb_loadTable.SelectedIndex]);
-            set_Make_Database_Button();
+            SetMakeDatabaseButton();
         }
 
         #endregion ADD/CLEAR Private Methods
diff --git a/ProteoformSuiteInternal/ComponentReader.cs b/ProteoformSuiteInternal/ComponentReader.cs
index 8452fae7..e219a4b7 100644
--- a/ProteoformSuiteInternal/ComponentReader.cs
+++ b/ProteoformSuiteInternal/ComponentReader.cs
@@ -124,7 +124,10 @@ public List<Component> remove_monoisotopic_duplicates_harmonics_from_same_scan(L
                     foreach (double missedMonoMass in possibleMissedMonoisotopicsList)
                     {
                         double massTolerance = missedMonoMass / 1000000d * Sweet.lollipop.raw_component_mass_tolerance;
-                        List<Component> missedMonoisotopics = scanComps.Where(cp => !removeThese.Contains(cp) && cp.weighted_monoisotopic_mass >= (missedMonoMass - massTolerance) && cp.weighted_monoisotopic_mass <= (missedMonoMass + massTolerance)).ToList(); // this is a list of harmonics to hc
+                        List<Component> missedMonoisotopics = scanComps.Where(cp => 
+                            !removeThese.Contains(cp) 
+                            && cp.weighted_monoisotopic_mass >= (missedMonoMass - massTolerance) 
+                            && cp.weighted_monoisotopic_mass <= (missedMonoMass + massTolerance)).ToList(); // this is a list of harmonics to hc
 
                         foreach (Component c in missedMonoisotopics.Where(m => m.id != sc.id).ToList())
                         {
@@ -164,7 +167,10 @@ public List<Component> remove_monoisotopic_duplicates_harmonics_from_same_scan(L
                     foreach (double harmonicMass in possibleHarmonicList)
                     {
                         double massTolerance = harmonicMass / 1000000d * Sweet.lollipop.raw_component_mass_tolerance;
-                        List<Component> harmonics = scanComps.Where(cp => !removeThese.Contains(cp) && cp.weighted_monoisotopic_mass >= (harmonicMass - massTolerance) && cp.weighted_monoisotopic_mass <= (harmonicMass + massTolerance)).ToList(); // this is a list of harmonics to hc
+                        List<Component> harmonics = scanComps.Where(cp => 
+                            !removeThese.Contains(cp) 
+                            && cp.weighted_monoisotopic_mass >= (harmonicMass - massTolerance) 
+                            && cp.weighted_monoisotopic_mass <= (harmonicMass + massTolerance)).ToList(); // this is a list of harmonics to hc
                         List<Component> someHarmonics = harmonics.Where(harmonicComponent => harmonicComponent.id != hc.id).ToList();
                         foreach (Component h in someHarmonics) // now that we have a list of harmonics to hc, we have to figure out what to do with them
                         {
diff --git a/ProteoformSuiteInternal/CytoscapeScript.cs b/ProteoformSuiteInternal/CytoscapeScript.cs
index 800020b3..d08f6ac6 100644
--- a/ProteoformSuiteInternal/CytoscapeScript.cs
+++ b/ProteoformSuiteInternal/CytoscapeScript.cs
@@ -618,7 +618,7 @@ public static void write_styles(List<ProteoformFamily> all_families, string styl
                 writer.WriteEndElement();
 
                 //NODE PROPERTIES
-                double max_total_intensity = quantitative != null ?
+                double max_total_intensity = all_families.Count == 0 ? 0 : quantitative != null ?
                     (double)all_families.SelectMany(f => f.experimental_proteoforms).Max(p => p.quant.intensitySum) :
                     all_families.SelectMany(f => f.experimental_proteoforms).Max(p => p.agg_intensity);
                 writer.WriteStartElement("node");
diff --git a/ProteoformSuiteInternal/ResultsSummaryGenerator.cs b/ProteoformSuiteInternal/ResultsSummaryGenerator.cs
index abdaaed5..1763b800 100644
--- a/ProteoformSuiteInternal/ResultsSummaryGenerator.cs
+++ b/ProteoformSuiteInternal/ResultsSummaryGenerator.cs
@@ -192,8 +192,8 @@ public static string proteoform_families_report()
 
             int raw_quant_components_in_fams = identified_families.Concat(ambiguous_families).Concat(unidentified_families).Sum(f => f.experimental_proteoforms.Sum(e => e.lt_quant_components.Count + e.hv_quant_components.Count));
             report += raw_quant_components_in_fams + "\tRaw Quantitative Components in Families" + Environment.NewLine;
-            report += Sweet.lollipop.raw_experimental_components.Count > 0 ?
-                Math.Round(100 * ((double)raw_quant_components_in_fams / (double)Sweet.lollipop.raw_experimental_components.Count), 2) + "\t% of Raw Quantitative Components in Families" + Environment.NewLine :
+            report += Sweet.lollipop.raw_quantification_components.Count > 0 ?
+                Math.Round(100 * ((double)raw_quant_components_in_fams / (double)Sweet.lollipop.raw_quantification_components.Count), 2) + "\t% of Raw Quantitative Components in Families" + Environment.NewLine :
                 "N/A\t% of Raw Quantitative Components in Families" + Environment.NewLine;
             report += Environment.NewLine;
 
diff --git a/ProteoformSuiteInternal/Sweet.cs b/ProteoformSuiteInternal/Sweet.cs
index db94f776..e39b378d 100644
--- a/ProteoformSuiteInternal/Sweet.cs
+++ b/ProteoformSuiteInternal/Sweet.cs
@@ -14,6 +14,7 @@ public class Sweet
     {
 
         public static Lollipop lollipop = new Lollipop();
+        public static string methodFilePath = "";
         public static List<string> save_actions = new List<string>();
         public static List<string> loaded_actions = new List<string>();
 
@@ -103,8 +104,9 @@ private static void add_actions(XmlWriter writer)
             }
         }
 
-        public static bool open_method(string alltext, bool add_files, out string warning_message)
+        public static bool open_method(string methodFilePath, string alltext, bool add_files, out string warning_message)
         {
+            Sweet.methodFilePath = methodFilePath;
             warning_message = "";
             loaded_actions.Clear();
             FieldInfo[] lollipop_fields = typeof(Lollipop).GetFields();
@@ -143,6 +145,8 @@ public static bool open_method(string alltext, bool add_files, out string warnin
                 field.SetValue(lollipop, Convert.ChangeType(value, type));
             }
 
+            lollipop.results_folder = !lollipop.results_folder.StartsWith(".") ? lollipop.results_folder : Path.GetFullPath(Path.Combine(Path.GetDirectoryName(methodFilePath), lollipop.results_folder));
+
             foreach (XElement action in action_elements)
             {
                 loaded_actions.Add(GetAttribute(action, "action"));
@@ -151,7 +155,7 @@ public static bool open_method(string alltext, bool add_files, out string warnin
             if (loaded_actions.Any(a => !a.StartsWith("add file ") && !a.StartsWith("change file ") && !a.StartsWith("shift ") && !a.StartsWith("accept ") && !a.StartsWith("unaccept ")))
                 return false;
 
-            if (add_files)  add_files_from_presets(lollipop.input_files); 
+            if (add_files) add_files_from_presets(lollipop.input_files); 
             else update_files_from_presets(lollipop.input_files);
             return true;
         }
@@ -162,12 +166,12 @@ public static bool open_method(string alltext, bool add_files, out string warnin
 
         public static void add_file_action(InputFile file)
         {
-            save_actions.Add("add file " + file.complete_path + " with purpose " + file.purpose.ToString());
+            save_actions.Add("add file '" + file.complete_path + "' with purpose " + file.purpose.ToString());
         }
 
         public static void change_file(InputFile file, object property, string property_name, string from, string to)
         {
-            save_actions.Add("change file " + file.complete_path + " property " + property_name + " of type " + property.GetType().FullName + " from " + from + " to " + to);
+            save_actions.Add("change file '" + file.complete_path + "' with purpose " + file.purpose + " property " + property_name + " of type " + property.GetType().FullName + " from " + from + " to " + to);
         }
 
         public static void accept_peak_action(IMassDifference peak)
@@ -187,12 +191,13 @@ public static void shift_peak_action(DeltaMassPeak peak)
 
         public static void add_files_from_presets(List<InputFile> destination)
         {
-            Regex findaddfile = new Regex(@"add file (\S+)");
-            Regex findpurpose = new Regex(@"purpose (.+)");
+            Regex findaddfile = new Regex(@"(add file ')(.+)(' with purpose )");
+            Regex findpurpose = new Regex(@"( purpose )(.+)");
             foreach (string add_file in loaded_actions.Where(x => x.StartsWith("add file ")))
             {
-                string filepath = findaddfile.Match(add_file).Groups[1].ToString();
-                Purpose? purpose = ExtensionMethods.EnumUntil.GetValues<Purpose>().FirstOrDefault(p => findpurpose.Match(add_file).Groups[1].ToString() == p.ToString());
+                string filestring = findaddfile.Match(add_file).Groups[2].ToString();
+                string filepath = !filestring.StartsWith(".") ? filestring : Path.GetFullPath(Path.Combine(Path.GetDirectoryName(methodFilePath), filestring));
+                Purpose? purpose = ExtensionMethods.EnumUntil.GetValues<Purpose>().FirstOrDefault(p => findpurpose.Match(add_file).Groups[2].ToString() == p.ToString());
                 if (purpose == null || !File.Exists(filepath))
                     continue;
                 string ext = Path.GetExtension(filepath);
@@ -203,17 +208,20 @@ public static void add_files_from_presets(List<InputFile> destination)
 
         public static void update_files_from_presets(List<InputFile> destination)
         {
-            Regex findchangefile = new Regex(@"change file (\S+)");
-            Regex findproperty = new Regex(@" property (\S+)");
-            Regex findtype = new Regex(@" type (\S+)");
-            Regex findto = new Regex(@" to (.+)"); // matches to end of line
+            Regex findchangefile = new Regex(@"(change file ')(.+)(' with purpose )");
+            Regex findpurpose = new Regex(@"( purpose )(.+)( property )");
+            Regex findproperty = new Regex(@"( property )(\S+)");
+            Regex findtype = new Regex(@"( type )(\S+)");
+            Regex findto = new Regex(@"( to )(.+)"); // matches to end of line
             foreach (string change_file in loaded_actions.Where(x => x.StartsWith("change file ")))
             {
-                string filename = Path.GetFileName(findchangefile.Match(change_file).Groups[1].ToString());
-                string property = findproperty.Match(change_file).Groups[1].ToString();
-                string typefullname = findtype.Match(change_file).Groups[1].ToString();
-                string value = findto.Match(change_file).Groups[1].ToString();
-                InputFile file = destination.FirstOrDefault(f => Path.GetFileName(f.complete_path) == filename); //match the filename, not the path, in case it changed folders
+                string filestring = findchangefile.Match(change_file).Groups[2].ToString();
+                string filepath = !filestring.StartsWith(".") ? filestring : Path.GetFullPath(Path.Combine(Path.GetDirectoryName(methodFilePath), filestring));
+                string property = findproperty.Match(change_file).Groups[2].ToString();
+                string typefullname = findtype.Match(change_file).Groups[2].ToString();
+                string value = findto.Match(change_file).Groups[2].ToString();
+                Purpose? purpose = ExtensionMethods.EnumUntil.GetValues<Purpose>().FirstOrDefault(p => findpurpose.Match(change_file).Groups[2].ToString() == p.ToString());
+                InputFile file = destination.FirstOrDefault(f => f.complete_path == filepath && f.purpose == purpose); //match the filename, not the path, in case it changed folders
                 PropertyInfo propertyinfo = typeof(InputFile).GetProperties().FirstOrDefault(p => p.Name == property);
                 Type type = Type.GetType(typefullname);
 
@@ -224,19 +232,19 @@ public static void update_files_from_presets(List<InputFile> destination)
             }
         }
 
-        private static Regex findmass = new Regex(@"mass (\S+)");
+        private static Regex findmass = new Regex(@"(mass )(\S+)");
         public static void mass_shifts_from_presets()
         {
-            Regex findshift = new Regex(@" by (.+)");
-            Regex findshiftrelationtype = new Regex(@"shift (\S+)");
+            Regex findshift = new Regex(@"( by )(.+)");
+            Regex findshiftrelationtype = new Regex(@"(shift )(\S+)");
             foreach (string mass_shift in loaded_actions.Where(x => x.StartsWith("shift ")))
             {
-                string relationshiptype = findshiftrelationtype.Match(mass_shift).Groups[1].ToString();
+                string relationshiptype = findshiftrelationtype.Match(mass_shift).Groups[2].ToString();
                 ProteoformComparison? comparison = ExtensionMethods.EnumUntil.GetValues<ProteoformComparison>().FirstOrDefault(x => relationshiptype == x.ToString());
-                bool converted = Double.TryParse(findmass.Match(mass_shift).Groups[1].ToString(), out double mass);
+                bool converted = Double.TryParse(findmass.Match(mass_shift).Groups[2].ToString(), out double mass);
                 if (comparison == null || !converted)
                     continue;
-                string shift = findshift.Match(mass_shift).Groups[1].ToString();
+                string shift = findshift.Match(mass_shift).Groups[2].ToString();
                 DeltaMassPeak peak = null;
                 if (comparison == ProteoformComparison.ExperimentalTheoretical)
                     peak = lollipop.et_peaks.FirstOrDefault(p => Math.Round(p.DeltaMass, 4) == Math.Round(mass, 4));
@@ -250,12 +258,12 @@ public static void mass_shifts_from_presets()
 
         public static void update_peaks_from_presets(ProteoformComparison comparison_to_update)
         {
-            Regex findacceptrelationtype = new Regex(@"accept (\S+)");
+            Regex findacceptrelationtype = new Regex(@"(accept )(\S+)");
             foreach (string peak_change in loaded_actions.Where(x => x.StartsWith("accept ") || x.StartsWith("unaccept ")))
             {
-                string relationshiptype = findacceptrelationtype.Match(peak_change).Groups[1].ToString();
+                string relationshiptype = findacceptrelationtype.Match(peak_change).Groups[2].ToString();
                 ProteoformComparison? comparison = ExtensionMethods.EnumUntil.GetValues<ProteoformComparison>().FirstOrDefault(x => relationshiptype == x.ToString());
-                bool converted = Double.TryParse(findmass.Match(peak_change).Groups[1].ToString(), out double mass);
+                bool converted = Double.TryParse(findmass.Match(peak_change).Groups[2].ToString(), out double mass);
                 if (comparison == null || comparison != comparison_to_update || !converted)
                     continue;
                 DeltaMassPeak peak = null;
diff --git a/README.md b/README.md
index 9513d02a..2da85c0b 100644
--- a/README.md
+++ b/README.md
@@ -3,6 +3,12 @@ Software for constructing, quantifying, and visualizing proteoform families.
 [![Build status](https://ci.appveyor.com/api/projects/status/qbc3xy4b35otnsxe/branch/master?svg=true)](https://ci.appveyor.com/project/stefanks/proteoform-suite/branch/master)
 [![Coverage Status](https://coveralls.io/repos/github/smith-chem-wisc/proteoform-suite/badge.svg?branch=master)](https://coveralls.io/github/smith-chem-wisc/proteoform-suite?branch=master)
 
+## Papers
+
+* [Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families. (2017, _J. Proteome Res._)](http://pubs.acs.org/doi/10.1021/acs.jproteome.7b00685)
+
+* [Elucidating _Escherichia coli_ Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database. (2017, _J. Proteome Res._)](http://pubs.acs.org/doi/abs/10.1021/acs.jproteome.7b00516)
+
 ## Latest Release and Vignette
 
 The latest release and vignette can be found [here](https://github.com/smith-chem-wisc/ProteoformSuite/releases/latest).
diff --git a/Test/TestDeltaMassPeak.cs b/Test/TestDeltaMassPeak.cs
index 6fd7ec5f..ecae9eca 100644
--- a/Test/TestDeltaMassPeak.cs
+++ b/Test/TestDeltaMassPeak.cs
@@ -294,7 +294,7 @@ public void shift_et_peak_neucode_from_actions()
             d2.mass_shifter = null;
             using (StreamWriter file = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml")))
                 file.WriteLine(Sweet.save_method());
-            Sweet.open_method(String.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out string warning);
+            Sweet.open_method(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), String.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out string warning);
             Sweet.mass_shifts_from_presets();
             d2.shift_experimental_masses(Convert.ToInt32(d2.mass_shifter), true);
 
diff --git a/Test/TestInputFile.cs b/Test/TestInputFile.cs
index ced992f8..ce1a7bfc 100644
--- a/Test/TestInputFile.cs
+++ b/Test/TestInputFile.cs
@@ -53,7 +53,7 @@ public void enter_directory_of_files_updated_with_presets()
             Sweet.change_file(mock, mock.biological_replicate, nameof(mock.biological_replicate), mock.biological_replicate.ToString(), "2");
             using (StreamWriter file = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml")))
                 file.WriteLine(Sweet.save_method());
-            Sweet.open_method(String.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out string warning);
+            Sweet.open_method(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), String.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out string warning);
             Sweet.lollipop.enter_input_files(folder, extension, purpose, destination, true);
             Assert.AreEqual(2, destination.Count);
             Assert.True(destination.All(f => f.extension == extension[0]));
@@ -74,7 +74,7 @@ public void add_file_from_presets()
             Sweet.change_file(mock, mock.biological_replicate, nameof(mock.biological_replicate), mock.biological_replicate.ToString(), "2");
             using (StreamWriter file = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml")))
                 file.WriteLine(Sweet.save_method());
-            Sweet.open_method(String.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out string warning);
+            Sweet.open_method(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), String.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out string warning);
             Sweet.add_files_from_presets(destination);
             Assert.AreEqual(1, destination.Count);
             Assert.True(destination[0].lt_condition == "Normal");
diff --git a/Test/TestLoadAndRun.cs b/Test/TestLoadAndRun.cs
index 305969fa..3f2fbcf2 100755
--- a/Test/TestLoadAndRun.cs
+++ b/Test/TestLoadAndRun.cs
@@ -1,5 +1,6 @@
 using NUnit.Framework;
 using ProteoformSuiteInternal;
+using System.IO;
 
 namespace Test
 {
@@ -42,7 +43,7 @@ public void test_load_and_run()
             Sweet.lollipop.ee_max_RetentionTime_difference = 2.5;
             Sweet.lollipop.peak_width_base_ee = 0.015;
             //load method --> should switch parametetrs to saved 
-            Sweet.open_method(saved_method, false, out string warning);
+            Sweet.open_method(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), saved_method, false, out string warning);
 
             //tests that the method settings properly a) saved b)loaded up above
             Assert.AreEqual(3, Sweet.lollipop.min_lysine_ct);
diff --git a/Test/TestSaveState.cs b/Test/TestSaveState.cs
index a2d64920..16824c81 100644
--- a/Test/TestSaveState.cs
+++ b/Test/TestSaveState.cs
@@ -61,7 +61,7 @@ public void restore_lollipop_settings()
                 else continue;
             }
 
-            Sweet.open_method(builder.ToString(), false, out string warning);
+            Sweet.open_method("", builder.ToString(), false, out string warning);
             foreach (PropertyInfo property in typeof(Lollipop).GetProperties())
             {
                 if (property.PropertyType == typeof(int))
@@ -120,7 +120,7 @@ public void test_accept_from_presets()
             Sweet.unaccept_peak_action(pr2);
             using (StreamWriter file = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml")))
                 file.WriteLine(Sweet.save_method());
-            Sweet.open_method(String.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out string warning);
+            Sweet.open_method(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"), String.Join(Environment.NewLine, File.ReadAllLines(Path.Combine(TestContext.CurrentContext.TestDirectory, "method.xml"))), true, out string warning);
             Sweet.lollipop.ee_peaks = test_community.accept_deltaMass_peaks(prs2, new List<ProteoformRelation>());
             Assert.AreEqual(1, Sweet.lollipop.ee_peaks.Count);
             DeltaMassPeak peak = Sweet.lollipop.ee_peaks[0];
diff --git a/Vignettes/Identification, Quantification, and Visualization of Yeast Proteoforms/protein_list_170807.txt b/Vignettes/Identification, Quantification, and Visualization of Yeast Proteoforms/protein_list_170807.txt
new file mode 100644
index 00000000..37a13240
--- /dev/null
+++ b/Vignettes/Identification, Quantification, and Visualization of Yeast Proteoforms/protein_list_170807.txt	
@@ -0,0 +1,1766 @@
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N,info:occupancy=0.00(1/2239)];#aa92[Calcium on D,info:occupancy=0.00(1/3867)];#aa87[Deamidation on N,info:occupancy=0.00(1/3867)];#aa97[TriMethylation,info:occupancy=0.00(1/4068)];#aa92[Fe[II] on D,info:occupancy=0.00(1/3867)];#aa67[Methyl on E,info:occupancy=0.00(1/2239)];#aa92[Oxidation on D,info:occupancy=0.00(1/3867)];#aa77[Acetyllysine,info:occupancy=0.00(1/5452)];#aa67[Calcium on E,info:occupancy=0.00(1/2239)];#aa77[Carbamidomethyl,info:occupancy=0.00(1/5452)];#aa74[DiMethyl on N,info:occupancy=0.00(1/2239)];#aa90[Sodium on D,info:occupancy=0.00(1/3867)];#aa77[TriMethylation,info:occupancy=0.00(1/5452)];#aa90[Sodium on D,info:occupancy=0.00(1/3867)];#aa77[TriMethylation,info:occupancy=0.00(1/5452)];#aa90[Sodium on D,info:occupancy=0.00(1/3867)];#aa69[Deamidation on N,info:occupancy=0.00(1/2239)];#aa77[DiMethyl on K,info:occupancy=0.00(1/5452)];#aa90[Sodium on D,info:occupancy=0.00(1/3867)];#aa77[Acetyllysine,info:occupancy=0.00(1/5452)];#aa77[Acetyllysine,info:occupancy=0.00(1/5452)];#aa90[Oxidation on D,info:occupancy=0.00(1/3867)];#aa97[Acetyllysine,info:occupancy=0.00(1/4068)];#aa77[Carbamidomethyl,info:occupancy=0.00(1/5452)];#aa92[Oxidation on D,info:occupancy=0.00(1/3867)];#aa90[Fe[III] on D,info:occupancy=0.00(1/3867)];#aa97[Hex on K,info:occupancy=0.00(1/4068)];#aa88[Hex on T,info:occupancy=0.00(1/3867)];#aa90[Fe[III] on D,info:occupancy=0.00(1/3867)];#aa80[Hex on T,info:occupancy=0.00(1/3867)];#aa90[Fe[III] on D,info:occupancy=0.00(1/3867)];#aa92[Sodium on D,info:occupancy=0.00(1/3867)];#aa77[TriMethylation,info:occupancy=0.00(1/5452)];#aa77[TriMethylation,info:occupancy=0.00(1/5452)];#aa74[Methyl on N,info:occupancy=0.00(1/2239)];#aa90[Fe[III] on D,info:occupancy=0.00(1/3867)];#aa69[Deamidation on N,info:occupancy=0.00(1/2239)];#aa90[Sodium on D,info:occupancy=0.00(1/3867)];#aa100[Acetylserine,info:occupancy=0.00(1/2682)];#aa101[Oxidation on P,info:occupancy=0.00(1/2682)];#aa97[Glucosylgalactosyl,info:occupancy=0.00(1/4068)];#aa97[Glucosylgalactosyl,info:occupancy=0.00(1/4068)];#aa97[Glucosylgalactosyl,info:occupancy=0.00(1/4068)];#aa88[dHex(1)Hex(3)HexNAc(2) on T,info:occupancy=0.00(1/3867)];#aa97[TriMethylation,info:occupancy=0.00(1/4068)];#aa80[dHex(1)Hex(3)HexNAc(2) on T,info:occupancy=0.00(1/3867)];#aa97[TriMethylation,info:occupancy=0.00(1/4068)];#aa67[Fe[III] on E,info:occupancy=0.00(1/2239)];#aa77[Acetyllysine,info:occupancy=0.00(1/5452)];#aa83[Ammonia loss,info:occupancy=0.00(1/3867)];#aa69[Deamidation on N,info:occupancy=0.00(1/2239)];#aa71[Methyl on Q,info:occupancy=0.00(1/2239)];#aa77[TriMethylation,info:occupancy=0.00(1/5452)];#aa67[Fe[III] on E,info:occupancy=0.00(1/2239)];#aa67[Fe[III] on E,info:occupancy=0.00(1/2239)];#aa67[Fe[III] on E,info:occupancy=0.00(1/2239)];#aa64[Fe[III] on D,info:occupancy=0.00(1/2239)];#aa91[DiMethyl on N,info:occupancy=0.00(1/3867)];#aa91[DiMethyl on N,info:occupancy=0.00(1/3867)];#aa91[DiMethyl on N,info:occupancy=0.00(1/3867)];#aa70[Fe[II] on E,info:occupancy=0.00(1/2239)];#aa77[Acetyllysine,info:occupancy=0.00(1/5452)];#aa70[Sodium on E,info:occupancy=0.00(1/2239)];#aa77[Carbamidomethyl,info:occupancy=0.00(1/5452)];#aa91[Deamidation on N,info:occupancy=0.00(1/3867)];#aa90[Sodium on D,info:occupancy=0.00(1/3867)];#aa105[Deamidation on N,info:occupancy=0.00(1/2682)];#aa105[Deamidation on N,info:occupancy=0.00(1/2682)];#aa92[Calcium on D,info:occupancy=0.00(1/3867)];#aa67[Fe[III] on E,info:occupancy=0.00(1/2239)];#aa69[Methyl on N,info:occupancy=0.00(1/2239)];#aa90[Sodium on D,info:occupancy=0.00(1/3867)];#aa91[Deamidation on N,info:occupancy=0.00(1/3867)];#aa90[Calcium on D,info:occupancy=0.00(1/3867)];#aa101[Oxidation on P,info:occupancy=0.00(1/2682)];#aa74[Deamidation on N,info:occupancy=0.00(1/2239)];#aa69[Deamidation on N,info:occupancy=0.00(1/2239)];#aa62[DiMethyl on N,info:occupancy=0.00(1/2239)];#aa74[Deamidation on N,info:occupancy=0.00(1/2239)];#aa83[Ammonia loss,info:occupancy=0.00(1/3867)];#aa91[Deamidation on N,info:occupancy=0.00(1/3867)];#aa83[Ammonia loss,info:occupancy=0.00(1/3867)];#aa91[Deamidation on N,info:occupancy=0.00(1/3867)];#aa83[Ammonia loss,info:occupancy=0.00(1/3867)];#aa91[Deamidation on N,info:occupancy=0.00(1/3867)];#aa83[Ammonia loss,info:occupancy=0.00(1/3867)];#aa91[Deamidation on N,info:occupancy=0.00(1/3867)];#aa83[Ammonia loss,info:occupancy=0.00(1/3867)];#aa91[Deamidation on N,info:occupancy=0.00(1/3867)];#aa69[DiMethyl on N,info:occupancy=0.00(1/2239)];#aa92[Oxidation on D,info:occupancy=0.00(1/3867)];#aa92[Oxidation on D,info:occupancy=0.00(1/3867)];#aa90[Sodium on D,info:occupancy=0.00(1/3867)];#aa92[Sodium on D,info:occupancy=0.00(1/3867)];#aa97[Hex on K,info:occupancy=0.00(1/4068)];#aa90[Sodium on D,info:occupancy=0.00(1/3867)];#aa92[Sodium on D,info:occupancy=0.00(1/3867)];#aa97[Hex on K,info:occupancy=0.00(1/4068)];#aa87[Deamidation on N,info:occupancy=0.00(1/3867)];#aa101[Dioxidation on P,info:occupancy=0.00(1/2682)];#aa69[DiMethyl on N,info:occupancy=0.00(1/2239)];#aa70[Fe[II] on E,info:occupancy=0.00(1/2239)];#aa77[Hex on K,info:occupancy=0.00(1/5452)];#aa67[Sodium on E,info:occupancy=0.00(1/2239)];#aa77[DiMethyl on K,info:occupancy=0.00(1/5452)];#aa92[Oxidation on D,info:occupancy=0.00(1/3867)];#aa90[Fe[II] on D,info:occupancy=0.00(1/3867)];#aa88[dHex(1)Hex(3)HexNAc(2) on T,info:occupancy=0.00(1/3867)];#aa92[Sodium on D,info:occupancy=0.00(1/3867)];#aa90[Fe[III] on D,info:occupancy=0.00(1/3867)];#aa105[Deamidation on N,info:occupancy=0.00(1/2682)];#aa107[DiMethyl on R,info:occupancy=0.00(1/2987)];#aa70[Sodium on E,info:occupancy=0.00(1/2239)];#aa90[Oxidation on D,info:occupancy=0.00(1/3867)];#aa88[Hex on T,info:occupancy=0.00(1/3867)];#aa97[Carbamidomethyl,info:occupancy=0.00(1/4068)];#aa80[Hex on T,info:occupancy=0.00(1/3867)];#aa97[Carbamidomethyl,info:occupancy=0.00(1/4068)];#aa101[Dioxidation on P,info:occupancy=0.00(1/2682)];#aa74[DiMethyl on N,info:occupancy=0.00(1/2239)];#aa77[TriMethylation,info:occupancy=0.00(1/5452)];#aa90[Methyl on D,info:occupancy=0.00(1/3867)];#aa85[Ammonia loss,info:occupancy=0.00(1/3867)];#aa97[Acetyllysine,info:occupancy=0.00(1/4068)];#aa87[Deamidation on N,info:occupancy=0.00(1/3867)];#aa97[Acetyllysine,info:occupancy=0.00(1/4068)];#aa77[Carbamidomethyl,info:occupancy=0.00(1/5452)];#aa85[Ammonia loss,info:occupancy=0.00(1/3867)];#aa91[Methyl on N,info:occupancy=0.00(1/3867)];#aa91[Methyl on N,info:occupancy=0.00(1/3867)];#aa90[Methyl on D,info:occupancy=0.00(1/3867)];#aa90[Oxidation on D,info:occupancy=0.00(1/3867)];#aa91[DiMethyl on N,info:occupancy=0.00(1/3867)];#aa97[Hex on K,info:occupancy=0.00(1/4068)];#aa87[Deamidation on N,info:occupancy=0.00(1/3867)];#aa90[Sodium on D,info:occupancy=0.00(1/3867)];#aa97[Hex on K,info:occupancy=0.00(1/4068)];#aa88[Hex on T,info:occupancy=0.00(1/3867)];#aa80[Hex on T,info:occupancy=0.00(1/3867)];#aa90[Fe[III] on D,info:occupancy=0.00(1/3867)];#aa70[Fe[III] on E,info:occupancy=0.00(1/2239)];#aa88[dHex(1)Hex(3)HexNAc(2) on T,info:occupancy=0.00(1/3867)];#aa70[Fe[III] on E,info:occupancy=0.00(1/2239)];#aa80[dHex(1)Hex(3)HexNAc(2) on T,info:occupancy=0.00(1/3867)];#aa74[DiMethyl on N,info:occupancy=0.00(1/2239)];#aa82[Oxidation on P,info:occupancy=0.00(1/3867)];#aa92[Sodium on D,info:occupancy=0.00(1/3867)];#aa90[Fe[III] on D,info:occupancy=0.00(1/3867)];#aa92[Oxidation on D,info:occupancy=0.00(1/3867)];#aa97[Hex on K,info:occupancy=0.00(1/4068)];#aa67[Methyl on E,info:occupancy=0.00(1/2239)];#aa91[DiMethyl on N,info:occupancy=0.00(1/3867)];#aa92[Sodium on D,info:occupancy=0.00(1/3867)];#aa77[Carbamidomethyl,info:occupancy=0.00(1/5452)];#aa87[Deamidation on N,info:occupancy=0.00(1/3867)];#aa74[Methyl on N,info:occupancy=0.00(1/2239)];#aa90[Fe[II] on D,info:occupancy=0.00(1/3867)];#aa77[Carbamidomethyl,info:occupancy=0.00(1/5452)];#aa97[DiMethyl on K,info:occupancy=0.00(1/4068)];
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