Label-free LC-MS/MS identification of phosphatidylglycerol-regulated proteins in Synechocystis sp. PCC6803

Tatjana Talamantes; Bettina Ughy; Ildikó Domonkos; Mihály Kis; Zoltán Gombos; Laszlo Prokai

doi:10.1002/pmic.201300372

Label-free LC-MS/MS identification of phosphatidylglycerol-regulated proteins in Synechocystis sp. PCC6803

Tatjana Talamantes, Bettina Ughy, Ildikó Domonkos, Mihály Kis, Zoltán Gombos, Laszlo Prokai

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

Abstract

We present a proteomics dataset combining SDS-PAGE prefractionation and data-dependent LC-MS/MS that enables the identification of phosphatidylglycerol-regulated proteins in the pgsA^- mutant of Synechocystis sp. PCC6803, a cyanobacterium strain that grows with this indispensable phospholipid added exogenously. We searched the acquired raw data against a composite protein sequence database of Synechocystis using MASCOT, and employed Progenesis LC-MS software for label-free quantification based on extracted peptide intensities to detect changes in protein abundances upon phospholipid withdrawal. Protein identifications were validated using rigorous criteria, and our analysis of the dataset revealed 80 phosphatidylglycerol-regulated proteins involved in various cellular processes including photosynthesis, respiration, metabolism, transport, transcription, and translation. The data have been deposited to the ProteomeXchange with identifier PXD000363 (http://proteomecentral.proteomexchange.org/dataset/PXD000363).

Original language	English
Pages (from-to)	1053-1057
Number of pages	5
Journal	Proteomics
Volume	14
Issue number	9
DOIs	https://doi.org/10.1002/pmic.201300372
State	Published - May 2014

Keywords

Bioinformatics
Cyanobacteria
GeLC-MS/MS
Phosphatidylglycerol
Quantitative label-free proteomics
Synechocystis

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title = "Label-free LC-MS/MS identification of phosphatidylglycerol-regulated proteins in Synechocystis sp. PCC6803",

abstract = "We present a proteomics dataset combining SDS-PAGE prefractionation and data-dependent LC-MS/MS that enables the identification of phosphatidylglycerol-regulated proteins in the pgsA- mutant of Synechocystis sp. PCC6803, a cyanobacterium strain that grows with this indispensable phospholipid added exogenously. We searched the acquired raw data against a composite protein sequence database of Synechocystis using MASCOT, and employed Progenesis LC-MS software for label-free quantification based on extracted peptide intensities to detect changes in protein abundances upon phospholipid withdrawal. Protein identifications were validated using rigorous criteria, and our analysis of the dataset revealed 80 phosphatidylglycerol-regulated proteins involved in various cellular processes including photosynthesis, respiration, metabolism, transport, transcription, and translation. The data have been deposited to the ProteomeXchange with identifier PXD000363 (http://proteomecentral.proteomexchange.org/dataset/PXD000363).",

keywords = "Bioinformatics, Cyanobacteria, GeLC-MS/MS, Phosphatidylglycerol, Quantitative label-free proteomics, Synechocystis",

author = "Tatjana Talamantes and Bettina Ughy and Ildik{\'o} Domonkos and Mih{\'a}ly Kis and Zolt{\'a}n Gombos and Laszlo Prokai",

year = "2014",

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doi = "10.1002/pmic.201300372",

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T1 - Label-free LC-MS/MS identification of phosphatidylglycerol-regulated proteins in Synechocystis sp. PCC6803

AU - Talamantes, Tatjana

AU - Ughy, Bettina

AU - Domonkos, Ildikó

AU - Kis, Mihály

AU - Gombos, Zoltán

AU - Prokai, Laszlo

PY - 2014/5

Y1 - 2014/5

N2 - We present a proteomics dataset combining SDS-PAGE prefractionation and data-dependent LC-MS/MS that enables the identification of phosphatidylglycerol-regulated proteins in the pgsA- mutant of Synechocystis sp. PCC6803, a cyanobacterium strain that grows with this indispensable phospholipid added exogenously. We searched the acquired raw data against a composite protein sequence database of Synechocystis using MASCOT, and employed Progenesis LC-MS software for label-free quantification based on extracted peptide intensities to detect changes in protein abundances upon phospholipid withdrawal. Protein identifications were validated using rigorous criteria, and our analysis of the dataset revealed 80 phosphatidylglycerol-regulated proteins involved in various cellular processes including photosynthesis, respiration, metabolism, transport, transcription, and translation. The data have been deposited to the ProteomeXchange with identifier PXD000363 (http://proteomecentral.proteomexchange.org/dataset/PXD000363).

AB - We present a proteomics dataset combining SDS-PAGE prefractionation and data-dependent LC-MS/MS that enables the identification of phosphatidylglycerol-regulated proteins in the pgsA- mutant of Synechocystis sp. PCC6803, a cyanobacterium strain that grows with this indispensable phospholipid added exogenously. We searched the acquired raw data against a composite protein sequence database of Synechocystis using MASCOT, and employed Progenesis LC-MS software for label-free quantification based on extracted peptide intensities to detect changes in protein abundances upon phospholipid withdrawal. Protein identifications were validated using rigorous criteria, and our analysis of the dataset revealed 80 phosphatidylglycerol-regulated proteins involved in various cellular processes including photosynthesis, respiration, metabolism, transport, transcription, and translation. The data have been deposited to the ProteomeXchange with identifier PXD000363 (http://proteomecentral.proteomexchange.org/dataset/PXD000363).

KW - Bioinformatics

KW - Cyanobacteria

KW - GeLC-MS/MS

KW - Phosphatidylglycerol

KW - Quantitative label-free proteomics

KW - Synechocystis

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SN - 1615-9853

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JO - Proteomics

JF - Proteomics

IS - 9

ER -

Label-free LC-MS/MS identification of phosphatidylglycerol-regulated proteins in Synechocystis sp. PCC6803

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