This talk concerns how to assign a peak in a fragment ion mass spectrum to a polypeptide sequence. This task is recognized to be problematic for some internal fragment ions, and as we will show, is problematic for all ion types (e.g., terminal fragments). Most experimental mass (peak) to theoretical database entry (molecule) correlations are delivered as a biproduct of automated...
The structural complexity and heterogeneity of monoclonal antibodies (mAbs) continue to pose analytical challenges. Over the past three decades, top-down (TD) and middle-down (MD) MS approaches have become powerful tools for characterizing intact antibodies and their subunits [1]. These methods are routinely applied in our CRO operations to complement intact mass and bottom-up proteomics,...
Top-Down Proteomics (TDP) has emerged as the dominant method for elucidating the intricacies of proteoform diversity, providing insights crucial for understanding biological processes. With development ranging from sample preparation to instrumentation, there has been a notable increase in research endeavors adopting and developing different TDP protocols that suit the objectives of the...
The new TDAuditor software generated quality metrics across the 1551 RAW files of the CTDP Blood Proteoform Atlas (BPA). The algorithm incorporates both spectral clustering and de novo sequence tagging. Multi-threading makes it possible to evaluate 100 mzMLs per minute on a standard desktop PC. The software produces reports in tab-delimited text and mzQC (JSON) formats.
The metrics...
Open data and science practices, including e.g. the FAIR (Findable, Accessible, Interoperable and Reusable) data principles, are widely implemented in the life sciences. Although this process started years later in proteomics than for other more established omics approaches (e.g. genomics and transcriptomics), their implementation in the field have enabled spectacular advances e.g. in...
