PXD016273

PXD016273 is an original dataset announced via ProteomeXchange.

Title	Comparative evaluation of different sample preparation workflows for reproducible, quantitative, and in-depth analysis of urine proteomics
Description	The growing field of urinary proteomics has provided a promising opportunity to identify biomarkers useful for diagnosis and prognostication of a number of diseases. Urine is abundant and readily collected in a non-invasive manner which makes it eminently available for testing, however sample preparation for proteomics analysis remains one of the biggest challenges in this field. As newer technologies to analyze tandem mass spectrometry (MS) data develop, utility of urinary proteomics would be enhanced by better sample processing and separation workflows to generate fast, reproducible, and more in-depth proteomics data. In this study, we have evaluated the performance of four sample preparation methods: MStern, PreOmics In-StageTip (iST), Suspension-trapping (S-Trap), and conventional urea In-Solution trypsin hydrolysis for non-depleted urine samples. Data Dependent Acquisition (DDA) mode on QE-HF was used for single-shot label-free data acquisition. Our results demonstrate a high degree of reproducibility within each workflow. PreOmics iST yields the best digestion efficiency with lowest percentage of missed-cleavage peptides. S-trap workflow gave the greatest number of peptide and protein identifications. Using S-trap method, with 0.5mL urine sample as starting material, we identify ~1500 protein groups and ~17700 peptides from DDA analysis with a single injection. The continued refinement of sample preparation (presented here), LC separation methods and mass spectrometry data acquisition can allow the integration of information rich urine proteomic records across large cohorts with other ‘big data’ initiatives becoming more popular in medical research.
HostingRepository	PRIDE
AnnounceDate	2020-03-06
AnnouncementXML	Submission_2020-03-05_23:13:28.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hossein Fazelinia
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-14 01:56:31	ID requested
⏵ 1	2020-03-05 23:13:29	announced

Ding H, Fazelinia H, Spruce LA, Weiss DA, Zderic SA, Seeholzer SH, Urine Proteomics: Evaluation of Different Sample Preparation Workflows for Quantitative, Reproducible, and Improved Depth of Analysis. J Proteome Res, 19(4):1857-1862(2020) [pubmed]

submitter keyword: urine proteomics, S-trap, preOmics iST, MStren, sample preparation, mass spectrometry, label-free, reproducibility

Steven H. Seeholzer
contact affiliation	Director of CHOP Proteomics Core Facility
contact email	SEEHOLZER@email.chop.edu
lab head
Hossein Fazelinia
contact affiliation	Children's Hospital of Philadelphia
contact email	fazeliniah@email.chop.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD016273
     1. Label: PRIDE project
     2. Name: Comparative evaluation of different sample preparation workflows for reproducible, quantitative, and in-depth analysis of urine proteomics