scholarly journals Arabidopsis proteome and the mass spectral assay library

2019 ◽  
Vol 6 (1) ◽  
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.

scholarly journals Arabidopsis Proteome and the Mass Spectral Assay Library

2019 ◽  
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.

scholarly journals Author Correction: Arabidopsis proteome and the mass spectral assay library

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Huoming Zhang ◽  
Pei Liu ◽  
Tiannan Guo ◽  
Huayan Zhao ◽  
Dalila Bensaddek ◽  
...  
Keyword(s):  
Mass Spectral ◽  
Arabidopsis Proteome

A Correction to this paper has been published: https://doi.org/10.1038/s41597-021-00852-8.

scholarly journals N-Linked Glycopeptide Identification Based on Open Mass Spectral Library Search

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Zhiwu An ◽  
Qingbo Shu ◽  
Hao Lv ◽  
Lian Shu ◽  
Jifeng Wang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Human Cancer ◽  
Cancer Cell Line ◽  
Peptide Identification ◽  
High Energy ◽  
Mass Spectral Library ◽  
Spectral Library ◽  
Data Set ◽  
Library Search ◽  
Mass Spectral

Confident characterization of intact glycopeptides is a challenging task in mass spectrometry-based glycoproteomics due to microheterogeneity of glycosylation, complexity of glycans, and insufficient fragmentation of peptide bones. Open mass spectral library search is a promising computational approach to peptide identification, but its potential in the identification of glycopeptides has not been fully explored. Here we present pMatchGlyco, a new spectral library search tool for intact N-linked glycopeptide identification using high-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS) data. In pMatchGlyco, (1) MS/MS spectra of deglycopeptides are used to create spectral library, (2) MS/MS spectra of glycopeptides are matched to the spectra in library in an open (precursor tolerant) manner and the glycans are inferred, and (3) a false discovery rate is estimated for top-scored matches above a threshold. The efficiency and reliability of pMatchGlyco were demonstrated on a data set of mixture sample of six standard glycoproteins and a complex glycoprotein data set generated from human cancer cell line OVCAR3.

scholarly journals Multi-Omics Characterization of Circular RNA-Encoded Novel Proteins Associated With Bladder Outlet Obstruction

2022 ◽  
Vol 9 ◽  
Author(s):  
Baoyi Zhu ◽  
Zhanfang Kang ◽  
Sihua Zhu ◽  
Yuying Zhang ◽  
Xiangmao Lai ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Quantitative Proteomics ◽  
Bladder Outlet Obstruction ◽  
Molecular Mechanisms ◽  
Outlet Obstruction ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Protein Profiles ◽  
Rt Pcr ◽  
Novel Proteins

Bladder outlet obstruction (BOO) is a common urologic disease associated with poorly understood molecular mechanisms. This study aimed to investigate the possible involvements of circRNAs (circular RNAs) and circRNA-encoded proteins in BOO development. The rat BOO model was established by the partial bladder outlet obstruction surgery. Differential expression of circRNA and protein profiles were characterized by deep RNA sequencing and iTRAQ quantitative proteomics respectively. Novel proteins encoded by circRNAs were predicted through ORF (open reading frame) selection using the GETORF software and verified by the mass spectrometry in proteomics, combined with the validation of their expressional alterations by quantitative RT-PCR. Totally 3,051 circRNAs were differentially expressed in bladder tissues of rat BOO model with widespread genomic distributions, including 1,414 up-regulated, and 1,637 down-regulated circRNAs. Our following quantitative proteomics revealed significant changes of 85 proteins in rat BOO model, which were enriched in multiple biological processes and signaling pathways such as the PPAR and Wnt pathways. Among them, 21 differentially expressed proteins were predicted to be encoded by circRNAs and showed consistent circRNA and protein levels in rat BOO model. The expression levels of five protein-encoding circRNAs were further validated by quantitative RT-PCR and mass spectrometry. The circRNA and protein profiles were substantially altered in rat BOO model, with great expressional changes of circRNA-encoded novel proteins.

scholarly journals Identifying Fentanyl with Mass Spectral Libraries

2021 ◽  
Author(s):  
Anthony J. Kearsley ◽  
Arun Moorthy
Keyword(s):  
Law Enforcement ◽  
Similarity Measures ◽  
Mass Spectral Library ◽  
Spectral Library ◽  
Mass Spectral ◽  
Fentanyl Analogs ◽  
Spectral Libraries ◽  
Mass Spectral Libraries

<div> <div> <div> <p>Synthesis, distribution and abuse of fentanyl, a synthetic opioid, has led to a critical worldwide epidemic. Mass spectral library searching for opioids remains unresolved despite being central to law-enforcement involving identification, monitoring and prosecution of opioid related crimes. In this article, two model problems are presented to illustrate difficulties associated with fentanyl identification. A collection of both currently-employed similarity measures and intuitive measures of dissimilarity are employed to simulate identifying fentanyl analogs with mass spectral library searching. </p> </div> </div> </div>

scholarly journals Changes in Protein Phosphorylation during Salivary Gland Degeneration in Haemaphysalis longicornis

2020 ◽  
Vol 58 (2) ◽  
pp. 161-171
Author(s):  
Qi Xiao ◽  
Yuhong Hu ◽  
Xiaohong Yang ◽  
Jianna Tang ◽  
Xiaoshuang Wang ◽  
...  
Keyword(s):  
Salivary Gland ◽  
Rna Interference ◽  
Protein Phosphorylation ◽  
Quantitative Study ◽  
Quantitative Proteomics ◽  
Blood Feeding ◽  
Study Data ◽  
Haemaphysalis Longicornis ◽  
Phosphorylated Proteins ◽  
Data Independent Acquisition

The ticks feed large amount of blood from their hosts and transmit pathogens to the victims. The salivary gland plays an important role in the blood feeding. When the female ticks are near engorgement, the salivary gland gradually loses its functions and begins to rapidly degenerate. In this study, data-independent acquisition quantitative proteomics was used to study changes in the phosphorylation modification of proteins during salivary gland degeneration in <i>Haemaphysalis longicornis</i>. In this quantitative study, 400 phosphorylated proteins and 850 phosphorylation modification sites were identified. Trough RNA interference experiments, we found that among the proteins with changes in phosphorylation, apoptosis-promoting Hippo protein played a role in salivary gland degeneration.

scholarly journals Comparison of TIMS-PASEF quantitative proteomics data-analysis workflows using FragPipe, DIA-NN, and Spectronaut from a user's perspective

2021 ◽  
Author(s):  
Alejandro Fernandez-Vega ◽  
Federica Farabegoli ◽  
Maria Mercedes Alonso-Martinez ◽  
Ignacio Ortea
Keyword(s):  
Data Analysis ◽  
Quantitative Proteomics ◽  
Real Life ◽  
Analysis Tool ◽  
Proteomics Data ◽  
Mass Spectrometers ◽  
Data Independent Acquisition ◽  
Proteomics Experiment ◽  
Under Sampling ◽  
The One

Data-independent acquisition (DIA) methods have gained great popularity in bottom-up quantitative proteomics, as they overcome the irreproducibility and under-sampling limitations of data-dependent acquisition (DDA). diaPASEF, recently developed for the timsTOF Pro mass spectrometers, has brought improvements to DIA, providing additional ion separation (in the ion mobility dimension) and increasing sensitivity. Several studies have benchmarked different workflows for DIA quantitative proteomics, but mostly using instruments from Sciex and Thermo, and therefore, the results are not extrapolable to diaPASEF data. In this work, using a real-life sample set like the one that can be found in any proteomics experiment, we compared the results of analyzing PASEF data with different combinations of library-based and library-free analysis, combining the tools of the FragPipe suite, DIA-NN and including MS1-level LFQ with DDA-PASEF data, and also comparing with the workflows possible in Spectronaut. We verified that library-independent workflows, not so efficient not so long ago, have greatly improved in the recent versions of the software tools, and now perform as well or even better than library-based ones. We report here information so that the user who is going to conduct a relative quantitative proteomics study using a timsTOF Pro mass spectrometer can make an informed decision on how to acquire (diaPASEF for DIA analysis, or DDA-PASEF for MS1-level LFQ) the samples, and what can be expected depending on the data analysis tool used, among the different alternatives offered by the recently optimized tools for TIMS-PASEF data analysis.

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