PXD011755

PXD011755 is an original dataset announced via ProteomeXchange.

Title	Comparison of two solid-phase extraction (SPE) methods for the identification and quantification of porcine retinal protein markers by LC MS/MS
Description	Proper sample preparation protocols represent a critical step for LC-MS-based proteomic study designs and influence the speed, performance and automation of high-throughput data acquisition. The main objective of this study was to compare two commercial solid phase extraction (SPE)-based sample preparation protocols (comprising SOLAµTM HRP SPE spin plates from Thermo Fisher Scientific and ZIPTIP® C18 pipette tips from Merck Millipore) for analytical performance, reproducibility and analysis speed. The house swine represents a promising animal model for studying human eye diseases including glaucoma and provides excellent requirements for the qualitative and quantitative MS-based comparison in terms of ocular proteomics. In total 6 technical replicates of two protein fractions [extracted with 0.1% dodecyl-ß-maltoside (DDM) or 1% trifluoroacetic acid (TFA)] of porcine retinal tissues were subjected to in-gel trypsin digestion and purified with both SPE-based workflows (N=3) prior to LC-MS analysis. On average, 550±70 proteins (1512±199 peptides) and 305±48 proteins (806±144 peptides) were identified from DDM and TFA protein fractions, respectively, after ZIPTIP® purification, and SOLAµTM workflow resulted in the detection of 513±55 proteins (1347±180 peptides) and 300±33 proteins (722±87 peptides), respectively (FDR<1%). Venn diagram analysis revealed an average overlap of 65±2% (DDM fraction) and 69±4% (TFA fraction) in protein identifications between both SPE-based methods. Quantitative analysis of 25 glaucoma-related protein markers also showed no significant differences (P>0.05) regarding protein recovery between both SPE methods. However, only glaucoma-associated marker MECP2 showed a significant (P=0.02) higher abundance in ZIPTIP®-purified replicates in comparison to SOLAµTM-treated study samples. Nevertheless, this result was not confirmed in the verification experiment using in-gel trypsin digestion of recombinant MECP2 (P=0.24). In conclusion, both SPE-based purification methods worked equally well in terms of analytical performance and reproducibility, whereas the analysis speed and the semi automation of the SOLAµTM spin plates workflow is much more convenient in comparison to the ZIPTIP® C18 method.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:50:11.577.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Carsten Schmelter
SpeciesList	scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-20 01:38:04	ID requested
1	2018-12-03 06:57:38	announced
2	2018-12-04 04:08:15	announced	Updated project metadata.
3	2018-12-07 00:00:08	announced	Updated project metadata.
⏵ 4	2024-10-22 04:50:13	announced	2024-10-22: Updated project metadata.

10.3390/ijms19123847;

Schmelter C, Funke S, Treml J, Beschnitt A, Perumal N, Manicam C, Pfeiffer N, Grus FH, Comparison of Two Solid-Phase Extraction (SPE) Methods for the Identification and Quantification of Porcine Retinal Protein Markers by LC-MS/MS. Int J Mol Sci, 19(12):(2018) [pubmed]

curator keyword: Technical

submitter keyword: Mass spectrometry

Glaucoma animal model

Biomarkers

Sample clean-up

ZIPTIP® C18 pipette tips

SOLAμTM HRP SPE spin plates

Carsten Schmelter
contact affiliation	Experimental Ophthalmology, Medical Care Center in Mainz, Germany
contact email	cschmelter@eye-research.org
lab head
Carsten Schmelter
contact affiliation	Universitätsmedizin Mainz
contact email	cschmelter@eye-research.org
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/12/PXD011755

PRIDE project URI

• PRIDE
  1. PXD011755
     1. Label: PRIDE project
     2. Name: Comparison of two solid-phase extraction (SPE) methods for the identification and quantification of porcine retinal protein markers by LC MS/MS