TY - JOUR A1 - Kuhring, M. A1 - Doellinger, J. A1 - Nitsche, A. A1 - Muth, Thilo A1 - Renard, B. Y. T1 - TaxIt: An Iterative Computational Pipeline for Untargeted Strain-Level Identification Using MS/MS Spectra from Pathogenic Single-Organism Samples JF - Journal of Proteome Research N2 - Untargeted accurate strain-level classification of a priori unidentified organisms using tandem mass spectrometry is a challenging task. Reference databases often lack taxonomic depth, limiting peptide assignments to the species level. However, the extension with detailed strain information increases runtime and decreases statistical power. In addition, larger databases contain a higher number of similar proteomes. We present TaxIt, an iterative workflow to address the increasing search space required for MS/MS-based strain-level classification of samples with unknown taxonomic origin. TaxIt first applies reference sequence data for initial identification of species candidates, followed by automated acquisition of relevant strain sequences for low level classification. Furthermore, proteome similarities resulting in ambiguous taxonomic assignments are addressed with an abundance weighting strategy to increase the confidence in candidate taxa. For benchmarking the performance of our method, we apply our iterative workflow on several samples of bacterial and viral origin. In comparison to noniterative approaches using unique peptides or advanced abundance correction, TaxIt identifies microbial strains correctly in all examples presented (with one tie), thereby demonstrating the potential for untargeted and deeper taxonomic classification. TaxIt makes extensive use of public, unrestricted, and continuously growing sequence resources such as the NCBI databases and is available under open-source BSD license at https://gitlab.com/rki_bioinformatics/TaxIt. KW - Bioinformatics KW - Mass spectrometry KW - Microbial proteomics KW - Strain identification KW - MS/MS PY - 2020 DO - https://doi.org/10.1021/acs.jproteome.9b00714 VL - 19 IS - 6 SP - 2501 EP - 2510 PB - ACS AN - OPUS4-50942 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Rhode, Michael A1 - Richter, Tim A1 - Mayr, P. A1 - Nitsche, A. A1 - Mente, Tobias A1 - Böllinghaus, Thomas T1 - Hydrogen diffusion in creep-resistant 9% Cr P91 multi-layer weld metal JF - Welding in the World N2 - Welded components of P91 9% Cr steel demand for careful welding fabrication with necessary post weld heat treatment (PWHT). Before the PWHT, a hydrogen removal heat treatment is necessary for avoidance of hydrogen assisted cracking (HAC). In this context, the microstructure and temperature-dependent hydrogen diffusion is important, and reliable diffusion coefficients of P91 weld metal are rare. For that reason, the diffusion behavior of P91 multi-layer weld metal was investigated for as-welded (AW) and PWHT condition by electrochemical permeation experiments at room temperature and carrier gas hot extraction (CGHE) from 100 to 400 °C. Hydrogen diffusion coefficients were calculated, and the corresponding hydrogen concentration was measured. It was ascertained that both heat treatment conditions show significant differences. At room temperature the AW condition showed significant hydrogen trapping expressed by to seven times lower diffusion coefficients. A preferred diffusion direction was found in perpendicular direction expressed by high permeability. The CGHE experiments revealed lower diffusion coefficients for the AW condition up to 400 °C. In this context, a hydrogen concentration of approximately 21 ml/100 g was still trapped at 100 °C. For that reason, a certain HAC susceptibility of as-welded P91 weld metal cannot be excluded, and hydrogen removal should be done before PWHT. KW - Creep resisting materials KW - Diffusion KW - Hydrogen KW - Weld metal KW - Post weld heat treatment KW - Microstructure PY - 2020 DO - https://doi.org/10.1007/s40194-019-00828-8 SN - 0043-2288 VL - 64 IS - 2 SP - 267 EP - 281 PB - Springer AN - OPUS4-50471 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Grossegesse, M. A1 - Hartkopf, F. A1 - Nitsche, A. A1 - Schaade, L. A1 - Doellinger, J. A1 - Muth, Thilo T1 - Perspective on Proteomics for Virus Detection in Clinical Samples JF - Journal of Proteome Research Special Issue: Proteomics in Pandemic Disease N2 - One of the most widely used methods to detect an acute viral infection in clinical specimens is diagnostic real-time polymerase chain reaction. However, because of the COVID-19 pandemic, mass-spectrometry-based proteomics is currently being discussed as a potential diagnostic method for viral infections. Because proteomics is not yet applied in routine virus diagnostics, here we discuss its potential to detect viral infections. Apart from theoretical considerations, the current status and technical limitations are considered. Finally, the challenges that have to be overcome to establish proteomics in routine virus diagnostics are highlighted. KW - COVID-19 KW - Mass spectrometry KW - Virus diagnostics KW - Virus detection KW - Targeted mass spectrometry KW - Proteomics PY - 2020 DO - https://doi.org/10.1021/acs.jproteome.0c00674 SN - 1535-3907 VL - 19 IS - 11 SP - 4380 EP - 4388 PB - ACS AN - OPUS4-51633 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -