PXD025897

PXD025897 is an original dataset announced via ProteomeXchange.

Title	Validation of filter aided sample preparation (FASP) approach for quantitative plant shotgun proteomics
Description	Gel-free LC-based shotgun proteomics represents the current gold standard of proteome analysis due to its outstanding throughput, analytical resolution and reproducibility. Thereby, the efficiency of sample preparation, i.e., protein isolation, solubilization and proteolysis, directly affects the correctness and reliability of quantification, being therefore the bottle neck of shotgun proteomics. The desired performance of the sample preparation protocols can be achieved by application of detergents. However, these ultimately compromise reverse phase chromatographic separation and disrupt electrospray ionization. Filter aided sample preparation (FASP) represents an elegant approach to overcome these limitations. Although this method is comprehensively validated for cell proteomics, its applicability to plants and compatibility with plant-specific protein isolation protocols is still unknown, i.e., no data on linearity of underlying protein quantification methods for plant matrices is available. To fill this gap, we address here the potential of FASP in combination with two protein isolation protocols for quantitative analysis of pea (Pisum sativum) seed and Arabidopsis thaliana leaf proteomes by the shotgun approach. For this, in comprehensive spiking experiments with bovine serum albumin (BSA), we evaluated the linear dynamic range (LDR) of protein quantification in the presence of plant matrices. Further, we addressed the interference of two different plant matrices in quantitative experiments, accomplished with two alternative sample preparation workflows in comparison to conventional FASP-based digestion of cell lysates, considered here as a reference. Our results indicate very good applicability of FASP to quantitative plant proteomics with an only limited impact of the protein isolation technique on the methods overall performance.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:38:22.405.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD025897
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Tatiana Leonova
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Pisum sativum (Garden pea); NCBI TaxID: 3888; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap XL

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-09 07:50:22	ID requested
1	2023-03-10 23:28:50	announced
⏵ 2	2023-11-14 08:38:24	announced	2023-11-14: Updated project metadata.

Leonova T, Ihling C, Saoud M, Frolova N, Rennert R, Wessjohann LA, Frolov A, Does filter-aided sample preparation provide sufficient method linearity for quantitative plant shotgun proteomics? Front Plant Sci, 13():874761(2022) [pubmed]

10.6019/PXD025897;

submitter keyword: plant proteomics, filter aided sample preparation (FASP), shotgun proteomics, LC-MS, phenol extraction, label-free quantification,Detergent-assisted proteolysis, sodium dodecyl sulfate

Andrej Frolov
contact affiliation	Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
contact email	afrolov@ipb-halle.de
lab head
Tatiana Leonova
contact affiliation	Leibniz-Institut of Plant Biochemistry
contact email	tleonova@ipb-halle.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD025897
     1. Label: PRIDE project
     2. Name: Validation of filter aided sample preparation (FASP) approach for quantitative plant shotgun proteomics