ASMS has come and gone another year. Whether you stopped by to see our booth, visited our lunch seminar, or discussed with the authors of our posters, we wanted to give you a short summary of the latest research that we presented at ASMS 2018.
As you might know, Biognosys is constantly pushing the boundaries of proteomics to achieve higher protein coverage and increased throughput, while also driving for higher analysis quality.
Higher Protein Coverage
A recent study of the growth-stimulating interaction between two stem cell types showed a number of differentially abundant secreted protein classes and demonstrated the feasibility to quantify the entire cellular proteome as well as thousands of secreted proteins with a data-independent analysis (DIA) approach. Using Hybrid Libraries, a term we use for the combination of large resource libraries and precise project libraries, we were able to increase the number of identified proteins while reducing the number of samples required for the analysis. This approach is particularly suited for applications when only a small amount of the sample is available to the researcher.
Quantification via DIA
If you are more interested in quantifying your proteins, PQ500™ might be of interest to you. Our PQ500™ peptide kit contains more than 800 SIS labeled peptides, allowing for absolute quantification of more than 500 human plasma proteins. However, the quantification can be expanded way beyond the reference peptides due to the density of the calibration curve non-reference proteins can be label-free quantified by using the absolute quantification of the reference peptides as anchor points. If human plasma is your area of interest, then you might want to know that we developed a new workflow, based on capillary flow techniques that are suited for high-throughput analysis. Thus, providing the researcher with a possibility to increase sample numbers, enabling higher statistical accuracy.
As proteomics is moving from discovery applications into clinical applications, the demand for high throughput techniques becomes more valuable. Millions of FFPE samples are available to researchers worldwide and we presented a novel workflow that allows the analysis of these samples in a robust manner. This will help researchers in identifying more biomarkers, especially in the field of oncology. But increasing the number of samples that we analyze, the need for a robust quality control becomes more important.
Effective quality control
One of the shortcomings in mass spectrometry-based research has always been that there is no unified quality control that monitors the various parameters during an experiment. Using Biognosys’ QuiC tool, we analyzed the one-year worth of mass spectrometry runs to identify predictive parameters for peptide-specific matches (PSM). Data from two different mass spectrometers suggest that MS2 count and MS1/MS2 medium intensity are strong indicators of performance and that they support the intuitive hypothesis that higher intensity spectra are of higher quality.
Another approach to improve on the number of correctly identified proteins is by using our Pulsar search engine, which is suited for DDA and DIA analysis. Pulsar has the capability to search raw data with FASTA files as well as with libraries and for our most recent analysis, we added normalized indexed retention times (iRTs) from available libraries to our library-based search. This approach proved especially valuable for single cell proteomics where limited amounts of sample material are available. With this approach, we have been able to increase the number of IDs between 23-27% on an experiment-wide level and up to 42% on an individual run level.
We hope you enjoyed ASMS 2018 and we look forward to welcoming you at one of our next conferences. We will be at IMSC in Florence next month, where we will be presenting our latest product so stay tuned for more information.