Iterative accumulation multiplexing Fourier transform ion cyclotron resonance mass spectrometry

Coded Apertures in Mass Spectrometry

The use of coded apertures in mass spectrometry can break the trade-off between throughput and resolution that has historically plagued conventional instruments. Despite their very early stage of development, coded apertures have been shown to increase throughput by more than one order of magnitude, with no loss in resolution in a simple 90-degree magnetic sector. This enhanced throughput can increase the signal level with respect to the underlying noise, thereby significantly improving sensitivity to low concentrations of analyte. Simultaneous resolution can be maintained, preventing any decrease in selectivity. Both one- and two-dimensional (2D) codes have been demonstrated. A 2D code can provide increased measurement diversity and therefore improved numerical conditioning of the mass spectrum that is reconstructed from the coded signal. This review discusses the state of development, the applications where coding is expected to provide added value, and the various instrument modifications necessary to implement coded apertures in mass spectrometers.

Order of Magnitude Signal Gain in Magnetic Sector Mass Spectrometry Via Aperture Coding

Miniaturizing instruments for spectroscopic applications requires the designer to confront a tradeoff between instrument resolution and instrument throughput [and associated signal-to-background-ratio (SBR)]. This work demonstrates a solution to this tradeoff in sector mass spectrometry by the first application of one-dimensional (1D) spatially coded apertures, similar to those previously demonstrated in optics. This was accomplished by replacing the input slit of a simple 90° magnetic sector mass spectrometer with a specifically designed coded aperture, deriving the corresponding forward mathematical model and spectral reconstruction algorithm, and then utilizing the resulting system to measure and reconstruct the mass spectra of argon, acetone, and ethanol. We expect the application of coded apertures to sector instrument designs will lead to miniature mass spectrometers that maintain the high performance of larger instruments, enabling field detection of trace chemicals and point-of-use mass spectrometry.

Multiplexed and data-independent tandem mass spectrometry for global proteome profiling

One of the most important early developments in the field of proteomics was the advent of automated data acquisition routines that allowed high-throughput unattended data acquisition during HPLC introduction of peptide mixtures to a tandem mass spectrometer. Prior to this, data acquisition was orders of magnitude less efficient being based entirely on lists of predetermined ions generated in a prior HPLC-MS experiment. This process, known generically as data-dependent analysis, empowered the development of shotgun proteomics where hundreds to thousands of peptide sequences are matched per experiment. In their most popular implementation, the most abundant ionized species from every precursor ion scan at each moment in chromatographic time are successively selected for isolation, activation and tandem mass analysis. While extremely powerful, this strategy has one primary limitation in that detectable dynamic range is restricted (in a top-down manner) to the peptides that ionize the best. To circumvent the serial nature of the data-dependent process and increase detectable dynamic range, the concepts of multiplexed and data-independent acquisition (DIA) have emerged. Multiplexed-data acquisition is based on more efficient co-selection and co-dissociation of multiple precursor ions in parallel, the data from which is subsequently de-convoluted to provide polypeptide sequences for each individual precursor ion. DIA has similar goals, but there is no real-time ion selection based on prior precursor ion scans. Instead, predefined m/z ranges are interrogated either by fragmenting all ions entering the mass spectrometer at every single point in chromatographic time; or by dividing the m/z range into smaller m/z ranges for isolation and fragmentation. These approaches aim to fully utilize the capabilities of mass spectrometers to maximize tandem MS acquisition time and to address the need to expand the detectable dynamic range, lower the limit of detection, and improve the overall confidence of peptide identifications and relative protein quantification measurements. This review covers all aspects of multiplexed- and data-independent tandem mass spectrometry in proteomics, from experimental implementations to advances in software for data interpretation.

Compressive mass analysis on quadrupole ion trap systems

Conventionally, quadrupole ion trap mass spectrometers eject ions of different mass-to-charge ratio (m/z) in a sequential fashion by performing a scan of the rf trapping voltage amplitude. Due to the inherent sparsity of most mass spectra, the detector measures no signal for much of the scan time. By exploiting this sparsity property, we propose a new compressive and multiplexed mass analysis approach--multi Resonant Frequency Excitation (mRFE) ejection. This new approach divides the mass spectrum into several mass subranges and detects all the subrange spectra in parallel for increased mass analysis speed. Mathematical estimation of standard mass spectrum is demonstrated while statistical classification on the parallel measurements remains viable because of the sparse nature of the mass spectra. This method can reduce mass analysis time by a factor of 3-6 and increase system duty cycle by 2×. The combination of reduced analysis time and accurate compound classification is demonstrated in a commercial quadrupole ion trap (QIT) system.