Clustering and Filtering Tandem Mass Spectra Acquired in Data-Independent Mode

Pak, Hui Song; Nikitin, Frédéric; Gluck, Florent; Lisacek, Frédérique; Scherl, Alexander; Müller, Markus

doi:10.1007/s13361-013-0720-z

Cited by 15 publications

(16 citation statements)

References 23 publications

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“…Additionally, DIA MS1 information (precursor peptide measurement scans) has not been systematically incorporated into DIA scoring so far, and the lack of accurate precursor mass leads to ambiguity in data interpretation, especially for peptides co-isolated in the same DIA window and sharing fragment ion peaks. Only a few computational tools 4, 18, 19 have been developed so far for untargeted peptide identification from DIA and they have not been tested on SWATH-like DIA methods nor are they capable of performing both identification and quantification.…”

Section: Introductionmentioning

confidence: 99%

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

et al. 2015

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Due to recent improvements in mass spectrometry (MS), there is an increased interest in data independent acquisition (DIA) strategies in which all peptides are systematically fragmented using wide mass isolation windows (“multiplex fragmentation”). DIA-Umpire (http://diaumpire.sourceforge.net/), a comprehensive computational workflow and open-source software for DIA data, detects precursor and fragment chromatographic features and assembles them into pseudo MS/MS spectra. These spectra can be identified using conventional database searching and protein inference tools, allowing sensitive untargeted analysis of DIA data without the need for a spectral library. Quantification is obtained using both precursor and fragment ion intensities. Furthermore, DIA-Umpire enables targeted extraction of quantitative information based on peptides initially identified in only a subset of the samples, resulting in more consistent quantification across multiple samples. We demonstrate the performance of the method using control samples of varying complexity, and publicly available glycoproteomics and affinity purification - mass spectrometry data.

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Section: Introductionmentioning

confidence: 99%

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

et al. 2015

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“…We centrally acquired high quality benchmarking data sets using different instrument platforms and acquisition modes, and focused our comparative analysis on five widely-used analysis tools for SWATH-MS data: four ‘peptide-centric’ query17 tools (OpenSWATH18, SWATH2.0, Skyline19, and Spectronaut20) and the ‘data-centric’ approach DIA-Umpire19. While the former use MS/MS libraries to extract groups of signals that reliably represent a specific peptide, followed by statistical methods to distinguish true from false matches14,18,21, the latter assembles “pseudo” tandem MS spectra that can be identified and quantified with conventional database-searching and protein-inference tools without an assay library8,22. All respective software developers participated in our study, ensuring an optimal analysis workflow and parameters for each SWATH software tool.…”

Section: Introductionmentioning

confidence: 99%

A multicenter study benchmarks software tools for label-free proteome quantification

et al. 2016

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The consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from SWATH-MS (sequential window acquisition of all theoretical fragment ion spectra), a method that uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test datasets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation windows setups. For consistent evaluation we developed LFQbench, an R-package to calculate metrics of precision and accuracy in label-free quantitative MS, and report the identification performance, robustness and specificity of each software tool. Our reference datasets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics.

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“…Analytical Methods PaperPublished on13 March 2014. Downloaded by University of Windsor on 26/06/2014 16:39:15.…”

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confidence: 99%

An effective integrated method for comprehensive identification of eighty-five compounds in Zhi-Zi-Da-Huang decoction by HPLC-DAD-ESI-MS (TOF) and HPLC-DAD-ESI-MS/MS (QqQ) without the help of reference standards

Ling-ling

Shi

et al. 2014

Anal. Methods

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decoction (ZZDHD) is an effective formula to treat alcoholic liver disease in China for nearly 2000 years. However, compounds in the formula are still not clear due to the complexity of the coexisting constituents. In this study, a sensitive integrated method based on HPLC-DAD-ESI-MS (TOF) and HPLC-DAD-ESI-MS/MS (QqQ) was developed and 85 chemical compounds in ZZDHD were identified. By TOF/MS, the quasi-molecular ions of the constituents were deduced according to the accurate mass of corresponding positive and negative ions, and product ion scan was then carried out using QqQ/MS. The fragments of each compound were observed by TOF/MS and/or QqQ/MS. Compounds with different chemical structures and concentration levels were tentatively identified according to their chromatographic retention time, UV absorption and MS data. Fragmentation patterns of six types were proposed to verify the identification results. It was found that at TOF/MS mode, a retro diels-alder (RDA) reaction occurred at bonds 1 and 3 in C-ring of flavanone 7-O-diglycosides when 4 0 -OH exists at B-ring. While the reaction was not observed if a methoxyl group appeared at the same site of flavanone skeleton. Another important phenomenon was noticed that 3-sinapoyl-5-caffeoylquinic acid, 4-sinapoyl-3-caffeoylquinic acid, and sinapylglucoside were detected only in ZZDHD while they were not found in four component herb extracts. The phenomenon revealed that changes of compounds happened when the component herbs were decocted together. The results in the paper are favorable of the clinic dosage and have laid a foundation for the subsequent research of ZZDHD in vivo.

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Clustering and Filtering Tandem Mass Spectra Acquired in Data-Independent Mode

Cited by 15 publications

References 23 publications

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

A multicenter study benchmarks software tools for label-free proteome quantification

An effective integrated method for comprehensive identification of eighty-five compounds in Zhi-Zi-Da-Huang decoction by HPLC-DAD-ESI-MS (TOF) and HPLC-DAD-ESI-MS/MS (QqQ) without the help of reference standards

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