Quantitative shotgun proteome, lipidome, and metabolome analysis by direct infusion

A method of analyzing a proteome using mass spectrometry, the method comprising the steps of:

• a) collecting a portion of a proteome from a cell;
• b) digesting the portion of the proteome to form a mixture of polypeptides;
• c) ionizing the mixture of polypeptides thereby generating ionized polypeptides;
• d) transporting the ionized polypeptides from an inlet side of a chamber to an outlet side of a chamber, wherein the chamber comprises a buffer gas and the ionized polypeptides are transported through the buffer gas;
• e) applying an electric field to the ionized polypeptides being transported through the buffer gas, and separating the ionized polypeptides according to ion mobility of the ionized polypeptides;
• f) transporting a portion of the separated ionized polypeptides through the outlet side of the chamber into a mass analyzer of a mass spectrometer device, wherein the chamber is in fluid connection with the mass analyzer;
• g) selectively isolating the portion of the separated ionized polypeptides in the mass analyzer according to the mass-to-charge ratios of the separated ionized polypeptides, thereby generating isolated ionized polypeptides;
• and
• h) measuring mass-to-charge ratios the isolated ionized polypeptides, thereby generating mass spectrometry data,
• wherein an online separation or purification step is not performed on the mixture of molecules or ionized molecules other than the ion mobility separation.

A method of analyzing a sample comprising one or more molecules using mass spectrometry, the method comprising the steps of:

• a) introducing the sample to an ionization source, thereby generating one or more ionized molecules;
• b) performing an ion filtering step on the ionized molecules comprising selectively transmitting a first portion of ionized molecules to a mass analyzer, wherein ionized molecules within the transmitted first portion of ionized molecules have an ion mobility within a first predefined ion mobility range;
• c) performing a mass filtering step comprising selectively isolating a first distribution of transmitted ions from the transmitted first portion of ionized molecules, wherein the isolated first distribution of transmitted ions have a mass-to-charge ratio within a first predefined mass-to-charge ratio range;
• d) generating mass spectrometry data comprising recording mass-to-charge ratios of the isolated first distribution of transmitted ions;
• and
• e) comparing the generated mass spectrometry data with one or more reference mass spectrometry data from a reference database, and identifying one or more target species of molecules from the sample as corresponding to a compound from the reference database.