TY  - JOUR
A1  - Tscheuschner, Georg
A1  - Kaiser, Melanie N.
A1  - Lisec, Jan
A1  - Beslic, Denis
A1  - Muth, Thilo
A1  - Krüger, Maren
A1  - Mages, Hans Werner
A1  - Dorner, Brigitte G.
A1  - Knospe, Julia
A1  - Schenk, Jörg A.
A1  - Sellrie, Frank
A1  - Weller, Michael G.
T1  - MALDI-TOF-MS-based identification of monoclonal murine Anti-SARS-CoV-2 antibodies within one hour
JF  - Antibodies
N2  - During the SARS-CoV-2 pandemic, many virus-binding monoclonal antibodies have been developed for clinical and diagnostic purposes. This underlines the importance of antibodies as universal bioanalytical reagents. However, little attention is given to the reproducibility crisis that scientific studies are still facing to date. In a recent study, not even half of all research antibodies mentioned in publications could be identified at all. This should spark more efforts in the search for practical solutions for the traceability of antibodies. For this purpose, we used 35 monoclonal antibodies against SARS-CoV-2 to demonstrate how sequence-independent antibody identification can be achieved by simple means applied to the protein. First, we examined the intact and light chain masses of the antibodies relative to the reference material NIST-mAb 8671. Already half of the antibodies could be identified based solely on these two parameters. In addition, we developed two complementary peptide mass fingerprinting methods with MALDI-TOF-MS that can be performed in 60 min and had a combined sequence coverage of over 80%. One method is based on the partial acidic hydrolysis of the protein by 5 mM of sulfuric acid at 99 degrees C. Furthermore, we established a fast way for a tryptic digest without an alkylation step. We were able to show that the distinction of clones is possible simply by a brief visual comparison of the mass spectra. In this work, two clones originating from the same immunization gave the same fingerprints. Later, a hybridoma sequencing confirmed the sequence identity of these sister clones. In order to automate the spectral comparison for larger libraries of antibodies, we developed the online software ABID 2.0. This open-source software determines the number of matching peptides in the fingerprint spectra. We propose that publications and other documents critically relying on monoclonal antibodies with unknown amino acid sequences should include at least one antibody fingerprint. By fingerprinting an antibody in question, its identity can be confirmed by comparison with a library spectrum at any time and context.
KW  - SARS-CoV-2 antibody
KW  - reproducibility crisis
KW  - peptide mass
KW  - fingerprinting
KW  - monoclonal antibody
KW  - traceability
KW  - identity
KW  - antibody
KW  - identification
KW  - antibody light chain
KW  - MALDI-TOF-MS
Y1  - 2022
U6  - https://doi.org/10.3390/antib11020027
SN  - 2073-4468
VL  - 11
IS  - 2
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Hirschfeld, Robert
A1  - Perscheid, Michael
A1  - Haupt, Michael
T1  - Explicit use-case representation in object-oriented programming languages
JF  - ACM SIGPLAN notices
N2  - Use-cases are considered an integral part of most contemporary development processes since they describe a software system's expected behavior from the perspective of its prospective users. However, the presence of and traceability to use-cases is increasingly lost in later more code-centric development activities. Use-cases, being well-encapsulated at the level of requirements descriptions, eventually lead to crosscutting concerns in system design and source code. Tracing which parts of the system contribute to which use-cases is therefore hard and so limits understandability.
 In this paper, we propose an approach to making use-cases first-class entities in both the programming language and the runtime environment. Having use-cases present in the code and the running system will allow developers, maintainers, and operators to easily associate their units of work with what matters to the users. We suggest the combination of use-cases, acceptance tests, and dynamic analysis to automatically associate source code with use-cases. We present UseCasePy, an implementation of our approach to use-case-centered development in Python, and its application to the Django Web framework.
KW  - design
KW  - languages
KW  - use-cases
KW  - separation of concerns
KW  - traceability
Y1  - 2012
U6  - https://doi.org/10.1145/2168696.2047856
SN  - 0362-1340
VL  - 47
IS  - 2
SP  - 51
EP  - 60
PB  - Association for Computing Machinery
CY  - New York
ER  -