Techniques for mass spectrometry peak list computation using parallel processing

Abstract

Described are techniques for processing data. Sample analysis is performed generating scans of data. Each scan comprises a set of data elements each associating an ion intensity count with a plurality of dimensions including a retention time dimension and a mass to charge ratio dimension. The scans are analyzed to identify one or more ion peaks. Analyzing includes filtering a first plurality of the scans producing a first plurality of filtered output scans. The filtering including first filtering producing a first filtering output, wherein the first filtering includes executing a plurality of threads in parallel which apply a first filter to the first plurality of scans to produce the first filtering output. Each of the plurality of threads computes at least one filtered output point for at least one corresponding input point included in the plurality of scans. Analyzing includes detecting one or more peaks using the filtered output scans.

Description

CROSS REFERENCES TO RELATED APPLICATIONS[0001]This application claims priority to U.S. Provisional Application No. 61 / 397,512 filed Jun. 11, 2011 Attorney Docket No. WCS-016PR1 / W-659, and U.S. Provisional Application No. 61 / 437,841 filed Jan. 31, 2011, Attorney Docket No WCS-016PR2 / W-659, both of which are incorporated by reference herein.BACKGROUND[0002]1. Technical Field[0003]This application relates generally to analysis of compounds, and, more particularly, to detection and quantification of ions collected by liquid chromatography, ion-mobility spectrometry and mass spectrometry.[0004]2. Description of Related Art[0005]Mass spectrometers (MS) are used widely for identifying and quantifying molecular species in a sample. During analysis, molecules from the sample are ionized to form ions that are introduced into the mass spectrometer for analysis. The mass spectrometer measures the mass-to-charge ratio (m / z) and intensity of the introduced ions.[0006]Mass spectrometers are limite...

AI Technical Summary

Benefits of technology

[0020]In accordance with one aspect of the invention is a method for processing data comprising performing sample analysis and generating scans of data, each of said scans comprising a set of data elements each associating an ion intensity count with a plurality of dimensions including a retention time dimension and a mass to charge ratio dimension; and analyzing said scans to identify one or more ion peaks, said analyzing including filtering a first plurality of said scans producing a first plurality of filtered output scans, said filtering including first filtering producing a first filtering output, wherein said first filtering includes executing a plurality of threads in parallel which apply a first filter to said first plurality of scans to produce said first filtering output, wherein each of said plurality of threads computes at least one filtered output point for at least one corresponding input point included in said plurality of scans; and detecting one or more peaks using said filtered output scans. The filtering may include performing first processing by a first of said plurality of threads, said first processing including applying a smoothing filter to a first input point in a mass-to-charge ratio dimension to produce a first filtered output point and applying a second derivative filter to the first input point in a mass-to-charge ratio dimension to produce a second filtered output point; and performing second processing by a second of said plurality of threads, said second processing including applying said smoothing filter to a second input point in a mass-to-charge ratio dimension to produce a third filtered output point and applying the second derivative filter to the second input point in a mass-to-charge ratio dimension to produce a fourth filtered output point, wherein said first thread and said second thread execute concurrently and said first thread and said second thread are included in a same block of threads accessing a plurality of input points including said first point and said second point from a portion of memory shared by said block of threads. The first plurality of threads may be included in a two-dimensional grid of thread blocks. Each of the thread blocks may include a two-dimensional configuration of threads in which each of the thread blocks is identified in said grid using a thread block identifier having an “x” dimension indexing said each thread block along the mass to charge ratio axis and having a “y” dimension indexing said each thread block along the retention time axis. The first thread may determine a first input point to which said smoothing filter is applied by said first thread. The first thread may determine a first output point identifying a location at which a corresponding filtered output point for said first input is stored. The first input point may be identified in said first plurality of scans in accordance with coordinates (m, s), wherein “m” is a mass coordinate mapping to a mass to charge ratio of said first input point and “s” identifies a scan in which said first input point is included. The first output point may also be identified using the coordinates (m,s). The first thread may be included in a first thread block having a first thread block identifier. The first thread may have a first thread identifier identifying a position of said first thread within said first thread block. The first thread may determine the coordinates (m,s) using said first thread block identifier and said first thread identifier. The first filtering may use filtering coefficients bound to a texture. The filtering coefficients may be used in connection with filtering a portion of less than all mass to charge ratio values in said first plurality of scans. The filtering may include executing a second plurality of threads concurrently, wherein each of said second plurality of threads applies a second filter in a retention time dimension to at least one data point. The second filter may be any of a smoothing filter and second derivative filter. The second filter may use a same set of filter coefficients for all data points to which the second filter is applied. The filter coefficients may be stored in constant memory used by a graphics processing unit. The graphics processing unit and said constant memory may be included in a separate device configured for used with a computer. The second plurality of threads may be included in a two-dimensional grid of thread blocks, each of said thread blocks being a two-dimensional block of threads. The method may also include determining first thread block dimensions of a first block of threads configured for parallel execution and each thread in said first block configured to apply a filter in a mass to charge ratio dimension to at least one data point; determining second thread block dimensions of a second block of threads configured for parallel execution and each thread in said second block configured to apply a filter in a retention time dimension to at least one data point; determining third thread block dimensions, wherein each dimension of said third thread block is a least common multiple of corresponding ones of said each dimension of said first thread block and said second thread block; and selecting scan pack dimensions in accordance with said third block dimensions, wherein said scan pack dimensions indicate sizing with respect to a number of said scans of data and a number of mass to charge ratio values per scan, wherein said analyzing is performed on a first scan pack before performing said analyzing with respect to a second scan pack, said first scan pack including a first portion of said scans of data and having said scan pack dimensions, said second scan pack including a second portion of said scans of data and having said scan pack dimensions. The first scan pack may include said first plurality of scans, and the method may further include reading, by executing code on a processing unit of a computer which executes instructions serially, said first scan pack; storing said first scan pack in a first memory of said computer; copying said first scan pack into a second memory of a device, said device including a graphics processing unit that performs parallel processing, wherein said second memory is configured for use by said graphics processing unit when performing parallel processing and wherein said first memory is not configured for use by said graphics processing unit; performing said first filtering by executing said plurality of threads in parallel on said graphics processor using said first scan pack to identify one or more peaks in said first scan pack; storing, by said graphics processing unit in said second memory, output data identifying said one or more peaks; and copying said output data from said second memory to said first memory. The step of detecting one or more peaks may be performed by concurrently executing threads included in a two-dimensional grid of thread blocks. Each of the thread blocks may include a two-dimensional configuration of threads. Threads included in a same first thread block may have access to data stored in a portion of memory shared by all threads in the first thread block. Each of the threads included in said two-dimensional grid may determine whether at least one filtered output point included in said filtered output scans is a peak. Each of the thread blocks may have first dimensions selected in accordance with utilization of a processing unit which performs concurrent processing, a number of threads included in said thread block having said first dimensions, and an approximation of said first dimensions to a square. The one or more peaks identified by said detecting may be identified with respect to retention time and mass to charge ratio dimensions. The plurality of dimensions may include an ion mobility dimension and the method may include identifying peaks with respect the ion mobility dimension. The analyzing may include identifying one or more properties for each of said one or more ion peaks identified. At least a first of said properties may be determined by concurrently executing threads included in a grid of thread blocks. Each of the threads may determine the first property for at least one of peaks identified by said detecting. The method may be performed in real-time while said scans are generated as a result of sample analysis by a mass spectrometer. The one or more peaks may be a first set of peaks and said analyzing may further comprise determining a scan pack si

Problems solved by technology

Mass spectrometers are limited in the number of different ions reliably detected and quantified within a single sample spectrum.

As a result, samples containing many molecular species may produce spectra that are too complex for interpretation or analysis using conventional mass spectrometers.

Moreover, at low concentration, ion detection suffers from background noise and/or interfering background molecules.

Co-elution of peaks from multiple molecules is one possible problem with this method of detecting peaks in a TIC.

Another difficulty encountered with peak detection is detector noise.

Aside from these problems, additional difficulties are encountered when conventional peak detection routines are used to detect chromatogra

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