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Amphitrite: A program for processing travelling wave ion mobility mass spectrometry data.

Sivalingam GN, Yan J, Sahota H, Thalassinos K - Int J Mass Spectrom (2013)

Bottom Line: We present a novel software package that enables the processing of T-Wave ion mobility data.It can also be used to automatically create a collision cross section (CCS) calibration and apply this to subsequent files of interest.A number of applications of the software, and how it enhances the information content extracted from the raw data, are illustrated using model proteins.

View Article: PubMed Central - PubMed

Affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK.

ABSTRACT

Since the introduction of travelling wave (T-Wave)-based ion mobility in 2007 a large number of research laboratories have embraced the technique, particularly those working in the field of structural biology. The development of software to process the data generated from this technique, however, has been limited. We present a novel software package that enables the processing of T-Wave ion mobility data. The program can deconvolute components in a mass spectrum and uses this information to extract corresponding arrival time distributions (ATDs) with minimal user intervention. It can also be used to automatically create a collision cross section (CCS) calibration and apply this to subsequent files of interest. A number of applications of the software, and how it enhances the information content extracted from the raw data, are illustrated using model proteins.

No MeSH data available.


Related in: MedlinePlus

Creation of a CCS calibration using denatured myoglobin. Amphitrite automatically selects charge states (panel A), which correspond to published CCS [41]. From the selected peaks, the ATDs are extracted and plotted in panel B, and the peak tops are automatically picked and displayed. A calibration curve, using a power fit to the data, is then calculated and plotted. Poor fits can be recalculated by manually adjusting the peak tops selected in the previous stage. The calibration procedure used has been described in [13].
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fig0010: Creation of a CCS calibration using denatured myoglobin. Amphitrite automatically selects charge states (panel A), which correspond to published CCS [41]. From the selected peaks, the ATDs are extracted and plotted in panel B, and the peak tops are automatically picked and displayed. A calibration curve, using a power fit to the data, is then calculated and plotted. Poor fits can be recalculated by manually adjusting the peak tops selected in the previous stage. The calibration procedure used has been described in [13].

Mentions: In Fig. 2, the process of creating a calibration is shown. From a user input perspective, the program is given the calibrant raw data file and the name of that calibrant, in this case myoglobin. Creating a calibration with more than one calibrant protein is also possible. It then automatically selects the charge states (vertical bands in Fig. 2A) that have corresponding published CCSs [41,42]. Low abundance charge state peaks can be deselected and ignored in order to improve the fit. The program automatically takes the highest intensity td to use in the calibration and produces the output shown in Fig. 2C. The calibration procedure used to create this figure has been published previously [13], however, alternative procedures [42] can also be calculated using Amphitrite. Outliers can be addressed by specifying alternate peak tops (which are also automatically detected), by specifically providing the td as input, or by removing it from the calibration.


Amphitrite: A program for processing travelling wave ion mobility mass spectrometry data.

Sivalingam GN, Yan J, Sahota H, Thalassinos K - Int J Mass Spectrom (2013)

Creation of a CCS calibration using denatured myoglobin. Amphitrite automatically selects charge states (panel A), which correspond to published CCS [41]. From the selected peaks, the ATDs are extracted and plotted in panel B, and the peak tops are automatically picked and displayed. A calibration curve, using a power fit to the data, is then calculated and plotted. Poor fits can be recalculated by manually adjusting the peak tops selected in the previous stage. The calibration procedure used has been described in [13].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4375678&req=5

fig0010: Creation of a CCS calibration using denatured myoglobin. Amphitrite automatically selects charge states (panel A), which correspond to published CCS [41]. From the selected peaks, the ATDs are extracted and plotted in panel B, and the peak tops are automatically picked and displayed. A calibration curve, using a power fit to the data, is then calculated and plotted. Poor fits can be recalculated by manually adjusting the peak tops selected in the previous stage. The calibration procedure used has been described in [13].
Mentions: In Fig. 2, the process of creating a calibration is shown. From a user input perspective, the program is given the calibrant raw data file and the name of that calibrant, in this case myoglobin. Creating a calibration with more than one calibrant protein is also possible. It then automatically selects the charge states (vertical bands in Fig. 2A) that have corresponding published CCSs [41,42]. Low abundance charge state peaks can be deselected and ignored in order to improve the fit. The program automatically takes the highest intensity td to use in the calibration and produces the output shown in Fig. 2C. The calibration procedure used to create this figure has been published previously [13], however, alternative procedures [42] can also be calculated using Amphitrite. Outliers can be addressed by specifying alternate peak tops (which are also automatically detected), by specifically providing the td as input, or by removing it from the calibration.

Bottom Line: We present a novel software package that enables the processing of T-Wave ion mobility data.It can also be used to automatically create a collision cross section (CCS) calibration and apply this to subsequent files of interest.A number of applications of the software, and how it enhances the information content extracted from the raw data, are illustrated using model proteins.

View Article: PubMed Central - PubMed

Affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK.

ABSTRACT

Since the introduction of travelling wave (T-Wave)-based ion mobility in 2007 a large number of research laboratories have embraced the technique, particularly those working in the field of structural biology. The development of software to process the data generated from this technique, however, has been limited. We present a novel software package that enables the processing of T-Wave ion mobility data. The program can deconvolute components in a mass spectrum and uses this information to extract corresponding arrival time distributions (ATDs) with minimal user intervention. It can also be used to automatically create a collision cross section (CCS) calibration and apply this to subsequent files of interest. A number of applications of the software, and how it enhances the information content extracted from the raw data, are illustrated using model proteins.

No MeSH data available.


Related in: MedlinePlus