IQuant: An automated pipeline for quantitative proteomics based upon isobaric tags

Wen, Bo; Zhou, Ruo; Feng, Qiang; Wang, Quanhui; Wang, Jun; Liu, Siqi

doi:10.1002/pmic.201300361

Cited by 230 publications

(145 citation statements)

References 33 publications

(47 reference statements)

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“…For protein identification, 20 ppm peptide mass tolerance was permitted for intact peptide masses and 0.05 Da for fragmented ions, with allowance for a maximum of two missed cleavages in the trypsin digests. Only unique peptides were quantitatively analyzed by using IQuant (Wen et al, ), with the median peptide ratio selected to represent the protein ratio. Proteins identified by at least two unique peptides and quantitatively detected in all four samples were used to further analyze the abundance change between control and fumigated adults.…”

Section: Methodsmentioning

confidence: 99%

Effects of terpinen‐4‐ol fumigation on protein levels of detoxification enzymes in Tribolium confusum

Liao

Shi

et al. 2019

Arch Insect Biochem Physiol

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Terpinen‐4‐ol has high fumigating activity to stored‐grain pests including Tribolium confusum. To understand the detoxification of terpinen‐4‐ol in insects, proteomic analysis was performed to identify related proteins and pathways in response to terpinen‐4‐ol fumigation in T. confusum. By using isobaric tags for relative and absolute quantitation (iTRAQ)‐based strategy, 4,618 proteins were obtained from T. confusum adults in the present study. Comparative proteomic analysis showed that 148 proteins were upregulated and 137 proteins were downregulated in beetles under the LC50 of terpinen‐4‐ol treatment for 24 hr. According to functional classifications, differentially expressed proteins (DEPs) were enriched in xenobiotic metabolism pathways. In the detoxification pathway, the levels of 25 cytochrome P450s, 5 glutathione S‐transferases, and 2 uridine diphosphate (UDP)‐glucuronosyltransferases were changed, most of which were upregulated in T. confusum exposed to terpinen‐4‐ol. The results indicated that terpinen‐4‐ol was potentially metabolized and detoxified by enzymes like P450s in T. confusum.

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Section: Methodsmentioning

confidence: 99%

Effects of terpinen‐4‐ol fumigation on protein levels of detoxification enzymes in Tribolium confusum

Liao

Shi

et al. 2019

Arch Insect Biochem Physiol

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“…All LC-ESI-MSMS analysis was based on the Triple TOF 5600 system (SCIEX, Framingham, MA, United States) fitted with a Nanospray III source (SCIEX, Framingham, MA, United States), and a pulled quartz tip as the emitter (New Objectives, Woburn, MA, United States). The IQuant software was used to conduct protein identification, tag impurity correction, data normalization, missing value imputation, protein ratio calculation, statistical analysis, and results presentation for iTRAQ (Wen et al, 2014). The three samples went through a batch of machine tests.…”

Section: Methodsmentioning

confidence: 99%

PLC-Mediated Signaling Pathway in Pollen Tubes Regulates the Gametophytic Self-incompatibility of Pyrus Species

Guan

Wang

et al. 2017

Front. Plant Sci.

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Among the Rosaceae species, the gametophytic self-incompatibility (GSI) is controlled by a single multi-allelic S locus, which is composed of the pistil-S and pollen-S genes. The pistil-S gene encodes a polymorphic ribonuclease (S-RNase), which is essential for identifying self-pollen. However, the S-RNase system has not been fully characterized. In this study, the self-S-RNase inhibited the Ca2+-permeable channel activity at pollen tube apices and the selectively decreased phospholipase C (PLC) activity in the plasma membrane of Pyrus pyrifolia pollen tubes. Self-S-RNase decreased the Ca2+ influx through a PLC-mediated signaling pathway. Phosphatidylinositol-specific PLC has a 26-amino acid insertion in pollen tubes of the ‘Jinzhuili’ cultivar, which is a spontaneous self-compatible mutant of the ‘Yali’ cultivar. ‘Yali’ plants exhibit a typical S-RNase-based GSI. Upon self-pollination, PLC gene expression is significantly higher in ‘Jinzhuili’ pollen tubes than that in ‘Yali’ pollen tubes. Moreover, the PLC in pollen tubes can only interact with one of the two types of S-RNase from the style. In the Pyrus x bretschneideri Rehd, the PLC directly interacted with the S7-RNase in the pollen tube, but not with the S34-RNase. Collectively, our results reveal that the effects of S-RNase on PLC activity are required for S-specific pollen rejection, and that PLC-IP3 participates in the self-incompatibility reaction of Pyrus species.

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“…The data analysis was performed by BGI using Mascot 2.3.02 combined with iQuant46. The Eucalyptus grandis (genome version 2.0, Phytozome) and Chrysoporthe austroafricana (Genbank JYIP00000000)47 predicted proteomes were combined in a concatenated protein database for the spectrum-database search (Table 2).…”

Section: Methodsmentioning

confidence: 99%

Evidence for salicylic acid signalling and histological changes in the defence response of Eucalyptus grandis to Chrysoporthe austroafricana

Zwart

Berger

Moleleki

et al. 2017

Sci Rep

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Eucalyptus species are cultivated for forestry and are of economic importance. The fungal stem canker pathogen Chrysoporthe austroafricana causes disease of varying severity on E. grandis. The Eucalyptus grandis-Chrysoporthe austroafricana interaction has been established as a model system for studying Eucalyptus antifungal defence. Previous studies revealed that the phytohormone salicylic acid (SA) affects the levels of resistance in highly susceptible (ZG14) and moderately resistant (TAG5) clones. The aims of this study were to examine histochemical changes in response to wounding and inoculation as well as host responses at the protein level. The anatomy and histochemical changes induced by wounding and inoculation were similar between the clones, suggesting that anatomical differences do not underlie their different levels of resistance. Tyloses and gum-like substances were present after inoculation and wounding, but cell death occurred only after inoculation. Hyphae of C. austroafricana were observed inside dead and living cells, suggesting that the possibility of a hemibiotrophic interaction requires further investigation. Proteomics analysis revealed the possible involvement of proteins associated with cell death, SA signalling and systemic resistance. In combination with previous information, this study forms a basis for future functional characterisation of candidate genes involved in resistance of E. grandis to C. austroafricana.

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IQuant: An automated pipeline for quantitative proteomics based upon isobaric tags

Cited by 230 publications

References 33 publications

Effects of terpinen‐4‐ol fumigation on protein levels of detoxification enzymes in Tribolium confusum

Effects of terpinen‐4‐ol fumigation on protein levels of detoxification enzymes in Tribolium confusum

PLC-Mediated Signaling Pathway in Pollen Tubes Regulates the Gametophytic Self-incompatibility of Pyrus Species

Evidence for salicylic acid signalling and histological changes in the defence response of Eucalyptus grandis to Chrysoporthe austroafricana

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