Exact p-value calculation for XCorr scoring of high-resolution MS/MS data.

Exact p-value (XPV)-based methods for dot product-like score functions-such as the XCorr score implemented in Tide, SEQUEST, Comet or shared peak count-based scoring in MSGF+ and ASPV-provide a fairly good calibration for peptide-spectrum-match (PSM) scoring in database searching-based MS/MS spectrum data identification. Unfortunately, standard XPV methods, in practice, cannot handle high-resolution fragmentation data produced by state-of-the-art mass spectrometers because having smaller bins increases the number of fragment matches that are assigned to incorrect bins and scored improperly. In this article, we present an extension of the XPV method, called the high-resolution exact p-value (HR-XPV) method, which can be used to calibrate PSM scores of high-resolution MS/MS spectra obtained with dot product-like scoring such as the XCorr. The HR-XPV carries remainder masses throughout the fragmentation, allowing them to greatly increase the number of fragments that are properly assigned to the correct bin and, thus, taking advantage of high-resolution data. Using four mass spectrometry data sets, our experimental results demonstrate that HR-XPV produces well-calibrated scores, which in turn results in more trusted spectrum annotations at any false discovery rate level.

From the archives of MD Anderson Cancer Center: Plasmablastic lymphoma presenting as a kidney mass in an immunocompetent patient: Case report and literature review.

BACKGROUND: Plasmablastic lymphoma (PBL) is a rare, aggressive large B-cell lymphoma with plasmablastic or immunoblastic morphology and a terminally differentiated B-cell immunophenotype. PBL often presents at extranodal sites, commonly the oral cavity of immunocompromised patients with human immunodeficiency virus (HIV) and/or Epstein-Barr virus (EBV) infection. Cases of PBL arising outside the oral cavity in previously healthy immunocompetent patients are rare. CASE REPORT: We report a 65-year-old HIV- and EBV-negative man who presented with abdominal pain, fatigue, and vomiting. Imaging studies showed a 30 × 18 cm bulky lobulated mass located within the left kidney with surrounding para-aortic lymphadenopathy. Serum and urine protein electrophoresis revealed a monoclonal gammopathy of IgA lambda type. Biopsy of the mass showed PBL. Bone marrow lumbar puncture evaluations also showed evidence of PBL. The patient was treated with chemotherapy and radiation with initial improvement; however, he died 14 months after initial diagnosis. CONCLUSIONS: Based on our literature review, this case of PBL is one of the few reported to present as a kidney mass in immunocompetent, HIV- and EBV-negative patient. Distinguishing PBL from plasma cell myeloma (PCM) can be challenging. Knowledge of clinical features including presence of CRAB (hypercalcemia, renal failure, anemia, bone lesions) or bone marrow infiltration by mature clonal plasma cells is helpful to establish a diagnosis of PCM. Genetic features of PCM (typical translocations or mutations) also can be helpful in distinguishing plasmablastic transformation of PCM and from PBL. The case we report also highlights the need for more studies to identify specific immunohistochemical and molecular markers to improve PBL diagnosis in immunocompetent patients.