Arabidopsis proteome v2.0

We developed a new resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about the Arabidopsis proteome, such as the significance of protein splice forms, post-translational modifications (PTMs), or simply obtain reliable information about specific proteins. PeptideAtlas is based on published mass spectrometry (MS) analyses collected through ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. All matched MS-derived peptide data are linked to spectral, technical and biological metadata. Nearly 40 million out of ~143 million MSMS spectra were matched to the reference genome Araport11, identifying ~0.5 million unique peptides and 17858 uniquely identified proteins (only isoform per gene) at the highest confidence level (FDR 0.0004; 2 non-nested peptides ≥ 9 aa each), assigned canonical proteins, and 3543 lower confidence proteins. Physicochemical protein properties were evaluated for targeted identification of unobserved proteins. Additional proteins and isoforms currently not in Araport11 were identified, generated from pseudogenes, alternative start, stops and/or splice variants and sORFs; these features should be considered for updates to the Arabidopsis genome. Phosphorylation can be inspected through a sophisticated PTM viewer. This new PeptideAtlas is integrated with community resources including TAIR, tracks in JBrowse, PPDB and UniProtKB. Subsequent PeptideAtlas builds will incorporate millions more MS data.

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Arabidopsis proteome and the mass spectral assay library

Scientific Data ◽

10.1038/s41597-019-0294-0 ◽

2019 ◽

Vol 6 (1) ◽

Cited By ~ 2

Author(s):

Huoming Zhang ◽

Pei Liu ◽

Tiannan Guo ◽

Huayan Zhao ◽

Dalila Bensaddek ◽

...

Keyword(s):

Quantitative Proteomics ◽

Model Organism ◽

Massively Parallel ◽

Spectral Library ◽

Mass Spectral ◽

Novel Proteins ◽

Data Independent Acquisition ◽

Arabidopsis Proteome ◽

Expression Atlas ◽

Targeted Approach

AbstractArabidopsis is an important model organism and the first plant with its genome completely sequenced. Knowledge from studying this species has either direct or indirect applications for agriculture and human health. Quantitative proteomics by data-independent acquisition mass spectrometry (SWATH/DIA-MS) was recently developed and is considered as a high-throughput, massively parallel targeted approach for accurate proteome quantification. In this approach, a high-quality and comprehensive spectral library is a prerequisite. Here, we generated an expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We applied DIA-MS using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups of which 1,787 were differentially expressed. MS data are available via ProteomeXchange with identifier PXD012708 and PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses.

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Mass-spectrometry-based draft of the Arabidopsis proteome

Nature ◽

10.1038/s41586-020-2094-2 ◽

2020 ◽

Vol 579 (7799) ◽

pp. 409-414 ◽

Cited By ~ 38

Author(s):

Julia Mergner ◽

Martin Frejno ◽

Markus List ◽

Michael Papacek ◽

Xia Chen ◽

...

Keyword(s):

Mass Spectrometry ◽

Arabidopsis Proteome

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Arabidopsis proteome responses to the smoke-derived growth regulator karrikin

Journal of Proteomics ◽

10.1016/j.jprot.2015.02.011 ◽

2015 ◽

Vol 120 ◽

pp. 7-20 ◽

Cited By ~ 20

Author(s):

Jana Baldrianová ◽

Martin Černý ◽

Jan Novák ◽

Petr L. Jedelský ◽

Eva Divíšková ◽

...

Keyword(s):

Growth Regulator ◽

Arabidopsis Proteome

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iTRAQ-based analysis of the Arabidopsis proteome reveals insights into the potential mechanisms of anthocyanin accumulation regulation in response to phosphate deficiency

Journal of Proteomics ◽

10.1016/j.jprot.2018.06.006 ◽

2018 ◽

Vol 184 ◽

pp. 39-53 ◽

Cited By ~ 7

Author(s):

Zhan Qi Wang ◽

Xiulian Zhou ◽

Lixiang Dong ◽

Jiena Guo ◽

Yueyue Chen ◽

...

Keyword(s):

Phosphate Deficiency ◽

Anthocyanin Accumulation ◽

Arabidopsis Proteome

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Arabidopsis Proteome and the Mass Spectral Assay Library

10.1101/665547 ◽

2019 ◽

Cited By ~ 1

Author(s):

Huoming Zhang ◽

Pei Liu ◽

Tiannan Guo ◽

Huayan Zhao ◽

Dalila Bensaddek ◽

...

Keyword(s):

Mass Spectrometry ◽

Abscisic Acid ◽

Acid Stress ◽

Model Organism ◽

Mass Spectrometry Data ◽

Mass Spectral ◽

Novel Proteins ◽

Data Independent Acquisition ◽

Arabidopsis Proteome ◽

Expression Atlas

AbstractArabidopsis is an important model organism and the first plant with its genome sequenced. Knowledge from studying this species has either direct or indirect applications to agriculture and human health. Quantitative proteomics by data-independent acquisition (SWATH/DIA-MS) was recently developed and considered as a high-throughput targetedlike approach for accurate proteome quantitation. In this approach, a high-quality and comprehensive library is a prerequisite. Here, we generated a protein expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We subsequently applied DIA-mass spectrometry using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups with 1,787 of them being differentially expressed which includes 65 proteins known to respond to abscisic acid stress. Mass spectrometry data are available via ProteomeXchange with identifier PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses.

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Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants

10.1101/867242 ◽

2019 ◽

Author(s):

Ryan W. Christian ◽

Seanna L. Hewitt ◽

Eric H. Roalson ◽

Amit Dhingra

Keyword(s):

Panicum Virgatum ◽

Higher Plants ◽

Gene Families ◽

Transcript Abundance ◽

Arabidopsis Proteome ◽

Genome Wide ◽

Plastid Targeting ◽

Wide Scale ◽

Scale Characterization ◽

Angiosperm Species

AbstractPlastids are morphologically and functionally diverse organelles that are dependent on nuclear-encoded, plastid-targeted proteins for all biochemical and regulatory functions. However, how plastid proteomes vary temporally, spatially, and taxonomically has been historically difficult to analyze at genome-wide scale using experimental methods. A bioinformatics workflow was developed and evaluated using a combination of fast and user-friendly subcellular prediction programs to maximize performance and accuracy for chloroplast transit peptides and demonstrate this technique on the predicted proteomes of 15 sequenced plant genomes. Gene family grouping was then performed in parallel using modified approaches of reciprocal best BLAST hits (RBH) and UCLUST. Between 628 protein families were found to have conserved plastid targeting across angiosperm species using RBH, and 828 using UCLUST. However, thousands of clusters were also detected where only one species had predicted plastid targeting, most notably in Panicum virgatum which had 1,458 proteins with species-unique targeting. An average of 45% overlap was found in plastid-targeted gene families compared with Arabidopsis, but an additional 20% of proteins matched against the full Arabidopsis proteome, indicating a unique evolution of plastid targeting. Neofunctionalization through subcellular relocalization is known to impart novel biological functions but has not been described before on genome-wide scale for the plastid proteome. Further work to correlate these predicted novel plastid-targeted proteins to transcript abundance and high-throughput proteomics will uncover unique aspects of plastid biology and shed light on how the plastid proteome has evolved to change plastid morphology and biochemistry.

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