Proteomics

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

ABSTRACT: 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.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): T Cell

SUBMITTER: Harshi Weerakoon  

LAB HEAD: Michelle M. Hill

PROVIDER: PXD019446 | Pride | 2020-10-19

REPOSITORIES: pride

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Dataset's files

Source:
Action DRS
Dataset_annotation_spectral_library.txt Txt
Human_Tcell_Consensus_Library.splib Other
Human_Tcell_peakview.tsv Tabular
SPLib1_HuTcell_01-1511242515.pepxml Pepxml
SPLib1_HuTcell_01.mzML Mzml
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A primary human T-cell spectral library to facilitate large scale quantitative T-cell proteomics.

Weerakoon Harshi H   Potriquet Jeremy J   Shah Alok K AK   Reed Sarah S   Jayakody Buddhika B   Kapil Charu C   Midha Mukul K MK   Moritz Robert L RL   Lepletier Ailin A   Mulvenna Jason J   Miles John J JJ   Hill Michelle M MM  

Scientific data 20201123 1

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  ...[more]

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