MRM triggered MRM, where the triggered MRM transitions make use of mobility device parameter values for the same compound, is performed. A plurality of primary MRM transitions are received and stored together with a mobility device parameter value for each transition as an MRM cycle list. Control information instructs a mobility device and a mass spectrometer to interrogate each MRM transition on the MRM cycle list within an MRM cycle of the mass spectrometer. If a product ion intensity value of an MRM transition exceeds a threshold value for a primary MRM transition, a plurality of secondary MRM transitions of the primary MRM transition with different mobility device parameter values are added to the MRM cycle list. The intensities of the measured secondary MRM transitions provide information on the optimum mobility device parameter for each compound.

An apparatus and a method of data independent combined ion mobility and mass spectroscopy analysis includes introducing precursor ions into an ion mobility spectrometer (IMS), sequentially releasing precursor ions from said IMS according to their ion mobility, introducing said released precursor ions into a mass filter, fragmenting the precursor ions transmitted through said mass filter to generate fragment ions, and carrying out a mass spectroscopy measurement on said fragment ions. The IMS and mass filter are controlled in a synchronized manner to carry out a plurality of IM scans, wherein adjacent mass windows in said IM scan that are associated with consecutive mass spectroscopy measurements of fragment ions overlap, such that precursor ions transmitted through said mass filter during said IM scan are located in at least one continuous scan region in an m/z-IM plane which extends in a generally diagonal direction in said m/z-IM plane.

Systems and methods are provided for identifying a precursor ion without using any a priori precursor ion information. In one method, a sample is analyzed using a tandem mass spectrometer, producing at least one measured product ion spectrum from a precursor mass-to-charge ratio range. The at least one measured product ion spectrum are received. A subset of measured product ions is selected from the at least one measured product ion spectrum. A list of candidate compounds is created by searching a dictionary of potential compounds that includes one or more predicted product ions for each of the potential compounds using the subset of measured product ions. A candidate compound on the list is selected as the identified compound. In another method, the measured product ions are assumed to correspond to shortened forms of the peptide and a protein database is searched for shortened forms of the peptide.

A method of mass spectrometry is disclosed comprising separating ions according to one or more physico-chemical properties. Ions which are onwardly transmitted to a Time of Flight mass analyzer are controlled by attenuating ions which would otherwise be transmitted to the Time of Flight mass analyzer and cause saturation of an ion detector and which have been determined or which are predicted to have a relatively high intensity.

Systems and methods are provided for identifying missing product ions after demultiplexing product ion spectra produced by overlapping precursor ion transmission windows in sequential windowed acquisition tandem mass spectrometry. Overlapping sequential windowed acquisition is performed on a sample. A first precursor mass window and the corresponding first product ion spectrum are selected from a plurality of overlapping stepped precursor mass windows and their corresponding product ion spectra. A product ion spectrum is demultiplexed for each overlapped portion of the first precursor mass window producing two or more demultiplexed first product ion spectra for the first precursor mass window. The two or more demultiplexed first product ion spectra are added together producing a reconstructed summed demultiplexed first product ion spectrum. Missing product ions are identified in the summed demultiplexed first product ion spectrum by comparing the summed demultiplexed first product ion spectrum and the first product ion spectrum.

A method is provided for detecting a polypeptide of interest in a plant without the use of a reference standard. The method comprises the steps of obtaining a plant expressing the polypeptide of interest and a negative control plant that does not express the polypeptide of interest, and analyzing a sample from each in an information-dependent acquisition (IDA) method. A method is also provided for determining the relative expression level of a polypeptide of interest in a plurality of plants without the use of a reference standard. This method comprises the steps of obtaining a plurality of plants expressing the polypeptide of interest and a negative control plant that does not express the polypeptide of interest, analyzing samples from each in an IDA method, and determining the relative expression level of the polypeptide in each of the plurality of plants.

The present invention provides a rapid, sensitive method for forensic drug testing in a post-mortem subject using oral fluid collected from the post-mortem subject. The method comprises collecting a sample of oral fluid from a post-mortem subject, analyzing the oral fluid sample qualitatively to detect the presence of one or more non-naturally occurring drugs, analyzing the oral fluid sample quantitatively to determine concentration of the one or more non-naturally occurring drugs in the post-mortem subject, and identifying the one or more non-naturally occurring drugs in the post-mortem subject. The detection and quantification in oral fluid is more sensitive and faster than detection and quantification of the non-naturally occurring drugs in blood, urine, bile, and liver tissue collected from the same post-mortem subject. Further, the qualitative and quantitative results are obtained in as little as three hours.

Systems and methods are provided for maximizing the data acquired from a sample in a mass spectrometry imaging experiment. An ion source device is instructed to produce and transmit to a tandem mass spectrometer a plurality of ions for each location of two or more locations of a sample. A mass range is divided into two or more mass window widths. For each location of the two or more locations, the tandem mass spectrometer is instructed to fragment the plurality of ions received for each location using each mass window width of the two or more mass window widths and to analyze resulting product ions. A product ion spectrum is produced for each mass window width, and a plurality of product ion spectra are produced for each location of the two or more locations.

Systems and methods are provided for shaping an effective transmission window used to select precursor ions for a precursor mass range of a sequential windowed acquisition experiment. For at least one precursor mass range, an ion transfer function is selected that is a function of mass using a processor. A quadrupole mass filter that transmits ions from a sample is instructed to produce two or more transmission windows over time using the processor. The two or more transmission windows are produced to cumulatively create an effective transmission window for the at least one precursor mass range with a shape described by the ion transfer function.

A phosphoprotein extraction method and a mass spectrometric method using a microbore hollow fiber enzymatic reactor (mHFER) based antigen-antibody reaction and, specifically, to an extraction method and a mass spectrometric method, wherein phosphoproteins or phosphopeptides present in the body are extracted using phosphoserine-, phosphothreonine-, and phosphotyrosine-antibodies, and measured by a mass spectrometer, and thus biomarker phosphoproteins for diagnosis of diseases are found, contributing to early diagnosis of diseases. The mass spectrometric method using the antigen-antibody reaction based extraction method can: minimize temporal and economic burdens resulting from a low extraction rate and a complicated sample pre-treatment; increase the extraction efficiency by using a considerable number of phosphopeptides (or phosphoproteins) and antibodies with strong affinity; and allow the extraction of low-concentration phosphopeptides or phosphoproteins, and thus is expected to have high applicability in discovering disease diagnosis protein markers and identifying and studying mechanisms thereof.