SWATH™ Data-Independent Acquisition Technology for the Detection of Host Cell Protein Contaminants in Biotherapeutics Protein Products

A method for detecting host cell contaminants in a protein biotherapeutic product using sequential windowed acquisition tandem mass spectrometry, comprising:

• performing sequential windowed acquisition on a protein biotherapeutic product sample by sequentially stepping a precursor mass window across a mass range, fragmenting transmitted precursor ions of each stepped precursor mass window, and analyzing product ions produced from the fragmented transmitted precursor ions using a tandem mass spectrometer, wherein the sequential windowed acquisition is performed without any information about contaminating proteins before data acquisition and wherein the sequential windowed acquisition produces data for every product ion of every transmitted precursor ion for the mass range;
• receiving one or more measured product ion spectra of the plurality of product ion spectra from the tandem mass spectrometer using a processor;
• comparing the one or more measured product ion spectra to a library of host cell proteins using the processor;
• and
• detecting one or more host cell contaminants by reporting host cell proteins from the library that match the one or more measured product ion spectra using the processor.

A computer program product, comprising a tangible computer-readable storage medium whose contents include a program with instructions being executed on a processor so as to perform a method for detecting host cell contaminants in a protein biotherapeutic product using sequential windowed acquisition tandem mass spectrometry, the method comprising:

• providing a system, wherein the system comprises one or more distinct software modules, and wherein the distinct software modules comprise a measurement module and a detection module;
• receiving one or more measured product ion spectra of a plurality of product ion spectra from a tandem mass spectrometer that performs sequential windowed acquisition on a protein biotherapeutic product sample by sequentially stepping a precursor mass window across a mass range, fragmenting transmitted precursor ions of each stepped precursor mass window, and analyzing product ions produced from the fragmented transmitted precursor ions using the measurement module, wherein the sequential windowed acquisition is performed without any information about contaminating proteins before data acquisition and wherein the sequential windowed acquisition produces the plurality of product ion spectra for the mass range;
• comparing the one or more measured product ion spectra to a library of host cell proteins using the detection module;
• and
• detecting one or more host cell contaminants by reporting host cell proteins from the library that match the one or more measured product ion spectra using the detection module.