private static void VerifyAdd(int numStaticMods, int numHeavyMods) { var calc = SkylineWindow.Document.Settings.PeptideSettings.Prediction.RetentionTime.Calculator as RCalcIrt; Assert.IsNotNull(calc); var standards = calc.GetStandardPeptides().Select(SequenceMassCalc.NormalizeModifiedSequence).ToArray(); var peptides = SkylineWindow.Document.PeptideGroups.First().Peptides.ToArray(); Assert.AreEqual(standards.Length, peptides.Length); foreach (var peptide in peptides) { Assert.IsTrue(standards.Contains(peptide.ModifiedTarget)); foreach (var transitionGroup in peptide.TransitionGroups) { var transitions = transitionGroup.Transitions.ToList(); for (var i = 1; i < transitions.Count; i++) { Assert.IsTrue(TransitionGroup.CompareTransitions(transitions[i - 1], transitions[i]) < 0); } } } var mods = SkylineWindow.Document.Settings.PeptideSettings.Modifications; Assert.AreEqual(numStaticMods, mods.StaticModifications.Count); Assert.AreEqual(numHeavyMods, mods.AllHeavyModifications.Count()); }