DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics

Midha, Mukul K.; Campbell, D. S.; Kapil, Charu; Kusebauch, Ulrike; Hoopmann, Michael R.; Bader, Samuel L.; Moritz, Robert L.

doi:10.1038/s41467-020-18901-y

Cited by 38 publications

(38 citation statements)

References 24 publications

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“…Over 62 parameters of compliance of the assay library was evaluated using DIALib-QC 32 ( http://www.swathatlas.org/DIALibQC.php ), a freely available tool that highlights the library’s complexity, characteristics, modifications, completeness and correctness ( Fig. 1 ) .…”

Section: Methodsmentioning

confidence: 99%

“…The library was generated from 209 measurements of unfractionated and fractionated E. coli cell lysates using OGE and differential ion mobility (DMS), overexpressed proteins, and synthetic peptides enabling deep proteome coverage on SCIEX TripleTOF 5600+ and 6600 instruments. This library has been statistically validated with MAYU 31 and its quality assessed with the spectral library tool DIALib-QC 32 ( www.swathatlas.org ) (Fig. 1 ).…”

Section: Background and Summarymentioning

confidence: 99%

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A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS

et al. 2020

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Data-Independent Acquisition (DIA) is a method to improve consistent identification and precise quantitation of peptides and proteins by mass spectrometry (MS). The targeted data analysis strategy in DIA relies on spectral assay libraries that are generally derived from a priori measurements of peptides for each species. Although Escherichia coli (E. coli) is among the best studied model organisms, so far there is no spectral assay library for the bacterium publicly available. Here, we generated a spectral assay library for 4,014 of the 4,389 annotated E. coli proteins using one- and two-dimensional fractionated samples, and ion mobility separation enabling deep proteome coverage. We demonstrate the utility of this high-quality library with robustness in quantitation of the E. coli proteome and with rapid-chromatography to enhance throughput by targeted DIA-MS. The spectral assay library supports the detection and quantification of 91.5% of all E. coli proteins at high-confidence with 56,182 proteotypic peptides, making it a valuable resource for the scientific community. Data and spectral libraries are available via ProteomeXchange (PXD020761, PXD020785) and SWATHAtlas (SAL00222-28).

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Section: Methodsmentioning

confidence: 99%

Section: Background and Summarymentioning

confidence: 99%

A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS

et al. 2020

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“…The in-house THP1 spectral assay library was evaluated using DIALib-QC [4] , a freely available software tool that highlights a library's complexity, characteristics, modifications, completeness and correctness available at http://www.swathatlas.org/DIALibQC.php . The DIALib-QC assessment report of the assay libraries is provided in Supplementary Table 2 .…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

THP1 proteomics in response to mycobacterium tuberculosis infection

2021

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Temporal data on how the mycobacterium infection establishes itself inside the host cell is not available. We differentiated human THP1 cell line with PMA and infected them with different laboratory (H37Ra and H37Rv) and clinical strains (BND433 and JAL2287) of mycobacterium tuberculosis (Mtb). Uninfected differentiated THP1 cells were used as infection control. Host proteome was investigated at four different time points to understand the dynamics of host response to mycobacterial infection with time. The investigated time points included 6 hrs, 18 hrs, 30 hrs and 42 hrs of infection with all the Mtb strains. SWATH-MS method was used to quantitate the host proteome in response to Mtb infection and the data thus obtained are available via PRIDE repository with the dataset identifier PXD022352 ( https://www.ebi.ac.uk/pride/archive/projects/PXD022352 ).

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“…We used spectrast2tsv (msproteomicstools 0.8.0) to generate the final assay library compatible with SWATH-MS windows from 300–2000 m/z mass range and for different SWATH-MS data analysis platforms. DIALib-QC v1.1 was used to assess the quality of these spectral libraries and to validate for theoretical m/z values correctness of both precursor and fragments ions in the libraries 19 . Decoy sequences were added to OpenSWATH assay library using OpenSWATH decoy generator 20 .…”

Section: Methodsmentioning

confidence: 99%

A primary human T-cell spectral library to facilitate large scale quantitative T-cell proteomics

et al. 2020

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Data independent analysis (DIA) exemplified by sequential window acquisition of all theoretical mass spectra (SWATH-MS) provides robust quantitative proteomics data, but the lack of a public primary human T-cell spectral library is a current resource gap. Here, we report the generation of a high-quality spectral library containing data for 4,833 distinct proteins from human T-cells across genetically unrelated donors, covering ~24% proteins of the UniProt/SwissProt reviewed human proteome. SWATH-MS analysis of 18 primary T-cell samples using the new human T-cell spectral library reliably identified and quantified 2,850 proteins at 1% false discovery rate (FDR). In comparison, the larger Pan-human spectral library identified and quantified 2,794 T-cell proteins in the same dataset. As the libraries identified an overlapping set of proteins, combining the two libraries resulted in quantification of 4,078 human T-cell proteins. Collectively, this large data archive will be a useful public resource for human T-cell proteomic studies. The human T-cell library is available at SWATHAtlas and the data are available via ProteomeXchange (PXD019446 and PXD019542) and PeptideAtlas (PASS01587).

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DIALib-QC an assessment tool for spectral libraries in data-independent acquisition proteomics

Cited by 38 publications

References 24 publications

A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS

A comprehensive spectral assay library to quantify the Escherichia coli proteome by DIA/SWATH-MS

THP1 proteomics in response to mycobacterium tuberculosis infection

A primary human T-cell spectral library to facilitate large scale quantitative T-cell proteomics

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