Testing lupus anticoagulants in a real-life scenario - a retrospective cohort study.

INTRODUCTION: Lupus anticoagulant (LAC) testing is challenging. Most data are derived from a well-controlled study environment with potential alterations to daily routines. The aim of this retrospective cohort study was to assess the capacity of various LAC screening tests and derived mixing tests to predict a positive result in subsequent confirmation tests in a large cohort of patients. MATERIALS AND METHODS: In 5832 individuals, we retrospectively evaluated the accuracy of the aPTT-A, aPTT-LAscreen, aPTT-FS and dRVVTscreen and of their derived mixing tests in detecting a positive confirmation test result within the same blood specimen. The group differences, degree of correlation and the predictive accuracy of LAC coagulation tests were analysed using the Mann-Whitney U test, the Spearman-rank-correlation and by area under the receiver operating characteristic curve (ROC-AUC) analysis. ROC-AUCs were compared with the Venkatraman´s permutation test. RESULTS: The pre-test probability of patients with clinically suspected LAC was 36% in patients without factor deficiency or anticoagulation therapy. The aPTT-LAscreen showed the best diagnostic accuracy with a ROC-AUC of 0.84 (95% CI: 0.82 - 0.86). No clear advantage of the dRVVT-derived mixing test was detectable when compared to the dRVVTscreen (P = 0.829). Usage of the index of circulating anticoagulant (ICA) did not improve the diagnostic power of respective mixing tests. CONCLUSIONS: Among the parameters evaluated, aPTT-LAscreen and derived mixing test parameters were the most accurate tests. In our study cohort, neither other mixing test nor the ICA presented any further advantage in LAC diagnostics.

Empirical multidimensional space for scoring peptide spectrum matches in shotgun proteomics.

Data-dependent tandem mass spectrometry (MS/MS) is one of the main techniques for protein identification in shotgun proteomics. In a typical LC-MS/MS workflow, peptide product ion mass spectra (MS/MS spectra) are compared with those derived theoretically from a protein sequence database. Scoring of these matches results in peptide identifications. A set of peptide identifications is characterized by false discovery rate (FDR), which determines the fraction of false identifications in the set. The total number of peptides targeted for fragmentation is in the range of 10,000 to 20,000 for a several-hour LC-MS/MS run. Typically, <50% of these MS/MS spectra result in peptide-spectrum matches (PSMs). A small fraction of PSMs pass the preset FDR level (commonly 1%) giving a list of identified proteins, yet a large number of correct PSMs corresponding to the peptides originally present in the sample are left behind in the "grey area" below the identity threshold. Following the numerous efforts to recover these correct PSMs, here we investigate the utility of a scoring scheme based on the multiple PSM descriptors available from the experimental data. These descriptors include retention time, deviation between experimental and theoretical mass, number of missed cleavages upon in-solution protein digestion, precursor ion fraction (PIF), PSM count per sequence, potential modifications, median fragment mass error, (13)C isotope mass difference, charge states, and number of PSMs per protein. The proposed scheme utilizes a set of metrics obtained for the corresponding distributions of each of the descriptors. We found that the proposed PSM scoring algorithm differentiates equally or more efficiently between correct and incorrect identifications compared with existing postsearch validation approaches.