The BioPharma Finder application can interpret high-resolution accurate mass (HRAM) LC-MS and LC-MS/MS data from collision-induced dissociation (CID), electron transfer dissociation (ETD), and higher-energy collision-induced dissociation (HCD) experiments carried out on Thermo Scientific™ instruments.
You can process LC-MS/MS runs using one of the following data acquisition methods:
- For an Orbitrap™ or LTQ™ FT instrument, acquire data using a high-resolution scan followed by several MS2 scans, either in high resolution or low resolution. The BioPharma Finder application can also process full-scan data (MS-only data).
- For an LCQ™/LTQ™ instrument, acquire the data in triple-play mode, for example, a full-scan followed by a data-dependent zoom scan or ultra-zoom scan, followed by a data-dependent MS2 scan in centroid mode.
The BioPharma Finder component detection algorithms determine the monoisotopic masses of component molecules using high-resolution full MS scan data. The application automatically uses associated MS2 spectra to confirm the oligonucleotide sequence, determine the site specific locations of modifications, and provide confirmation of expected and unexpected modifications. Furthermore, the component detection algorithms enable you to detect impurities or byproducts and perform comparative analysis and peak detection.
The ideal data acquisition for oligonucleotide characterization is described below:
- A high-resolution full MS scan producing isotopically-resolved data for the full-length oligonucleotide product. This data is used for component detection resulting in the deconvolution of the monoisotopic or average mass of the molecule.
- A data-dependent MS2 scan using higher-energy collision-induced dissociation (HCD), collision-induced dissociation (CID), or both to confirm the sequence of the molecule. Multiplexed targeted MS2 experiments can also be used to provide more complete sequence coverage as long as the full MS scan is also part of the data acquisition method.