Data acquisition and component identification - BioPharma Finder Software - Intact Mass Analysis User Guide - Data acquisition and component identification - Getting started - BioPharma Finder Software - BioPharma Finder Software

The BioPharma Finder application can interpret high-resolution accurate mass (HRAM) LC/MS and LC/MS/MS data from experiments carried out on Thermo Scientific instruments.

You can process LC/MS/MS runs using either of the following data acquisition methods:

• For an Orbitrap Exploris™ or Orbitrap Eclipse™ instrument, acquire data using a high-resolution scan followed by several MS/MS scans, in either high resolution or low resolution. The BioPharma Finder application can also process full-scan 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 MS/MS 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 MS/MS spectra to confirm the peptide, protein, or oligonucleotide sequence, determine the site-specific locations of modifications, and provide confirmation of expected and unexpected modifications. The application provides component identification using a novel prediction algorithm, relative quantitation of post-translational modifications (PTMs), and in-depth identification using error-tolerant searching, amino acid substitution, and de novo sequencing. Furthermore, the component detection algorithms enable you to detect impurities or metabolites and perform comparative analysis and peak detection.

The ideal data acquisition for protein characterization is described below:

• A high-resolution full MS scan producing isotopically-resolved data for the sequence. This data is used for component detection resulting in the deconvolution of the monoisotopic or average mass of the molecule.
• A data-dependent MS/MS scan using higher-energy collision-induced dissociation (HCD), collision-induced dissociation (CID), or both to confirm the sequence of the molecule. Multiplexed targeted MS/MS 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.