Using data-independent mass spectrometry to extend detectable dynamic range without prior fractionation

Young Ah Goo; David R. Goodlett

doi:10.1016/B978-0-12-818607-7.00018-9

Using data-independent mass spectrometry to extend detectable dynamic range without prior fractionation

Young Ah Goo, David R. Goodlett

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

Abstract

Data-dependent acquisition (DDA) is widely used in shotgun proteomics to profile the protein components of complex samples. Although very popular, it presents major drawbacks in terms of detectable dynamic range. We developed a data-independent acquisition (DIA) method, called precursor acquisition independent from ion count (PAcIFIC), which shows increased protein identification as well as extended detectable dynamic range over DDA methods. In this chapter, we discuss recent advances that have made PAcIFIC faster, more accurate, and quantitative. Currently, the time needed to perform a PAcIFIC experiment can be reduced to less than 2 days using an ion trap mass spectrometer with an overall tandem mass spectral acquisition rate of 0.2 s or less.

Original language	English
Title of host publication	Proteomic and Metabolomic Approaches to Biomarker Discovery
Publisher	Elsevier
Pages	327-337
Number of pages	11
ISBN (Electronic)	9780128186077
DOIs	https://doi.org/10.1016/B978-0-12-818607-7.00018-9
State	Published - Jan 1 2019

Keywords

Data-independent acquisition (DIA)
Dynamic range
Precursor acquisition independent from ion count (PAcIFIC)
Pseudo-MRM
Quantification

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10.1016/B978-0-12-818607-7.00018-9

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abstract = "Data-dependent acquisition (DDA) is widely used in shotgun proteomics to profile the protein components of complex samples. Although very popular, it presents major drawbacks in terms of detectable dynamic range. We developed a data-independent acquisition (DIA) method, called precursor acquisition independent from ion count (PAcIFIC), which shows increased protein identification as well as extended detectable dynamic range over DDA methods. In this chapter, we discuss recent advances that have made PAcIFIC faster, more accurate, and quantitative. Currently, the time needed to perform a PAcIFIC experiment can be reduced to less than 2 days using an ion trap mass spectrometer with an overall tandem mass spectral acquisition rate of 0.2 s or less.",

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AB - Data-dependent acquisition (DDA) is widely used in shotgun proteomics to profile the protein components of complex samples. Although very popular, it presents major drawbacks in terms of detectable dynamic range. We developed a data-independent acquisition (DIA) method, called precursor acquisition independent from ion count (PAcIFIC), which shows increased protein identification as well as extended detectable dynamic range over DDA methods. In this chapter, we discuss recent advances that have made PAcIFIC faster, more accurate, and quantitative. Currently, the time needed to perform a PAcIFIC experiment can be reduced to less than 2 days using an ion trap mass spectrometer with an overall tandem mass spectral acquisition rate of 0.2 s or less.

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KW - Pseudo-MRM

KW - Quantification

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M3 - Chapter

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SP - 327

EP - 337

BT - Proteomic and Metabolomic Approaches to Biomarker Discovery

PB - Elsevier

ER -

Using data-independent mass spectrometry to extend detectable dynamic range without prior fractionation

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Keywords

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