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

ABSTRACT: A comprehensive and high-quality E. coli spectral assay library for 56,182 proteotypic peptides mapped to 4,014 (91.5%) of the 4,389 annotated proteins using one- and two-dimensional fractionated samples, and ion mobility separation.

INSTRUMENT(S): TripleTOF 5600, TripleTOF 6600

ORGANISM(S): Escherichia Coli

TISSUE(S): Cell Culture

SUBMITTER: Mukul Midha

LAB HEAD: Prof. Robert L. Moritiz

PROVIDER: PXD020785 | Pride | 2020-10-19

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	20130113_Ecoli_IB_P04-P23_IDA_1.mzML	Mzml
	20130113_Ecoli_IB_P04-P23_IDA_1.wiff	Wiff
	20130113_Ecoli_IB_P04-P23_IDA_1.wiff.scan	Wiff
	20130113_Ecoli_IB_P12-P35_IDA_1.mzML	Mzml
	20130113_Ecoli_IB_P12-P35_IDA_1.wiff	Wiff

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

Midha Mukul K MK Kusebauch Ulrike U Shteynberg David D Kapil Charu C Bader Samuel L SL Reddy Panga Jaipal PJ Campbell David S DS Baliga Nitin S NS Moritz Robert L RL

Scientific data 20201112 1

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 ...[more]

PMID: 33184295

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

Project description:A comprehensive and high-quality E. coli spectral assay library for 56,182 proteotypic peptides mapped to 4,014 (91.5%) of the 4,389 annotated proteins using one- and two-dimensional fractionated samples, and ion mobility separation.

2020-10-19 | PXD020761 | Pride

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

Project description:Comprehensive spectral libraries are essential in sequential window acquisition of all theoretical mass spectra (SWATH-MS) based high throughput proteomic studies. Even though SWATH-MS assays provide robust quantitative proteomics data its applications to human T-cell studies are limited by the lack of a human T-cell spectral library. To address this resource gap, we generated a high-quality spectral library containing data for 3,941 unique proteins from primary human T-cells across genetically unrelated donors. SWATH-MS analysis of 18 primary T-cell samples using the new human T-cell spectral library identified and quantified 3,022 proteins at 1% FDR, whereas the larger Pan-human spectral library identified and quantified 2,794 proteins, with only 34% overlap. Combining the two libraries resulted in 4,061 proteins, covering ~50% of proteins in immune-related pathways. Overall, this data suggests DDA-MS is suited to discovery projects through to its enhanced sensitivity and SWATH-MS is suited to high-throughput projects.

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Qualitative and Quantitative proteomic analyses of Schistosoma japonicum Eggs and Egg-derived Secretory-Excretory proteins

Project description:Schistosome parasites lay up to a thousand eggs per day inside the veins of their mammalian hosts. The immature eggs deposited by females against endothelia of venules will embryonate within days. Approximately 30% of the eggs will migrate to the lumen of the intestine to continue the parasite life cycle. Many eggs, however, are trapped in the liver and intestine causing the main pathology associated with schistosomiasis mansoni and japonica, the liver granulomatous response. Excretory/Secretory egg proteins drive much of egg-induced pathogenesis of schistosomiasis mansoni, and Schistosoma japonicum induce a markedly distinct granulomatous response to that of S. mansoni.

2019-09-26 | PXD012835 | Pride

Meiotic Nuclear Pore Complex Modularity Provides Key Insights into Nuclear Basket Organization

Project description:Using phosphoproteomics and time-lapse fluorescence microscopy, we report that NPCs nuclear pore complexes (NPCs) undergo two distinct modularity events for the nucleoporins Nup60 and Nup2 during budding yeast meiosis: partial and full nuclear basket detachment.

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The DIALib-QC software tool for the systematic assessment of spectral library quality in data-independent acquisition proteomics

Project description:DIALib-QC (DIA library quality control) tool is used for the systematic evaluation of a spectral library’s characteristics, completeness and mass-accuracy ensuring correct identification and accurate quantitation of peptides and proteins from DIA/SWATH processing tools.

2020-10-16 | PXD020953 | Pride

Quantitative proteomic analysis of the hemolymph from Bithynia siamensis goniomphalos infected with Opisthorchis viverrini

Project description:We have performed a quantitative proteomic analysis of the hemocytes and plasma proteins from O. viverrini-infected Bithynia siamensis goniomphalos snails using SWATH-MS. The dataset contains validation SWATH-MS data and Skyline results plus the sample-specific libraries.

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DDA files of human cancer cells for the NCI-60 SWATH project PXD003539

Project description:This is the raw files for the DDA library used for intepreting the NCI-60 SWATH project PXD003539

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Reproducibility, specificity and accuracy of DIA quantification - OpenSWATH

Project description:Data dependent acquisition (DDA) is the method of choice for mass spectrometry based proteomics discovery experiments, data-independent acquisition (DIA) is steadily becoming more important. One of the most important requirement to perform a DIA analysis is the availability of spectral libraries for the peptide identification and quantification. Several researches were already conducted regarding the creation of spectral libraries from DDA analyses and obtaining identifications with these in DIA measurements. But so far only few experiments were conducted, to estimate the effect of these libraries on the quantitative level. In this work we created a spike-in gold standard dataset with known contents and ratios of proteins in a complex sample matrix. With this dataset, we first created spectral libraries using different sample preparation approaches with and without sample prefractionation on peptide and protein level. Two different search engines were used for protein identification. In total, five different spike-in states were compared with DIA analyses, comparing eight different spectral libraries generated by varying approaches and one library free method, as well as one default DDA analysis. Not only the number of identifications on peptide and protein level in the spectral libraries and the corresponding analyses was inspected, but also the number of expected and identified significant quantifications and their ratios were thoroughly examined. We found, that while libraries of prefractionationed samples are generally larger, the actually yielded identifications are not increased compared to repetitive non-fractionated measurements. Furthermore, we show that the accuracy of the quantifications is also highly dependent on the applied spectra library and also whether the peptide or protein level is analysed. Overall, the reproducibility and accuracy of DIA is superior to DDA in all analysed approaches.

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Yeast Phospho QTL (resubmission)

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