PXD008938-1

PXD008938 is an original dataset announced via ProteomeXchange.

Title	Barley leaf sample preparation
Description	Barley is an important cereal crop all over the world. Detailed molecular characterization of barley provides the basis for development of improved cultivars, stress and drought-resistant plants. We here present an LC-MS/MS-based proteomics study of barley leaf aimed at optimization of methods to achieve efficient and unbiased trypsin digestion of proteins prior to LC-MS/MS based sequencing and quantification of peptides. We evaluated two spin filter-aided sample preparation protocols using either sodium dodecyl-sulphate (SDS) or sodium deoxycholate (SDC), and three in-solution digestion (ISD) protocols using SDC or trichloroacetic acid/acetone precipitation. The proteomics workflow identified up to 1800 barley proteins based on sequencing of up to 7700 peptides per sample. The two spin filter-based protocols provided a 17-38% higher efficiency than the ISD protocols, including more proteins of low abundance. Among the ISD protocols, a simple one-step reduction and S-alkylation method (OP-ISD) was the most efficient for barley leaf sample preparation; it identified and quantified 1500 proteins and displayed higher peptide-to-protein inference ratio and higher average amino acid sequence coverage of proteins. The two spin filter-aided sample preparation protocols are compatible with TMT labeling for quantitative proteomics studies. They exhibited complementary performance as about 30% of the proteins were identified by either one or the other protocol, but also demonstrated a positive bias for membrane proteins when using SDC as detergent. We provide detailed protocols for efficient barley protein sample preparation for LC-MS/MS-based proteomics studies. Spin filter-based protocols are the most efficient for the preparation of barley leaf samples for MS-based proteomics, however, a simple protocol provides comparable results although with different peptide digestion profile.
HostingRepository	PRIDE
AnnounceDate	2018-09-03
AnnouncementXML	Submission_2018-09-03_02:04:42.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wei-Qing Wang
SpeciesList	scientific name: Hordeum vulgare (Barley); NCBI TaxID: 4513;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2018-02-13 01:25:05	ID requested
⏵ 1	2018-09-03 02:04:43	announced
2	2024-10-22 04:43:31	announced	2024-10-22: Updated project metadata.

Wang WQ, Jensen ON, M, ø, ller IM, Hebelstrup KH, Rogowska-Wrzesinska A, Evaluation of sample preparation methods for mass spectrometry-based proteomic analysis of barley leaves. Plant Methods, 14():72(2018) [pubmed]

curator keyword: Biological

submitter keyword: Hordeum vulgare, in solution digestion, mass spectrometer, sodium deoxycholate, sample preparation

Wei-Qing Wang
contact affiliation	Institute of Botany, the Chinese Academy of Sciences
contact email	wwq0814@ibcas.ac.cn
lab head
Wei-Qing Wang
contact affiliation	Institute of Botany, the Chinese Academy of Sciences
contact email	wwq0814@ibcas.ac.cn
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008938
     1. Label: PRIDE project
     2. Name: Barley leaf sample preparation