Project PXD001268

PRIDE Assigned Tags:
Biomedical Dataset
Dataset Belongs to:
Human Proteome Project
Download Project Files
Project Protein Table
Project Peptide Table
Visualize in PRIDE Inspector
Follow the next three steps to open your selected project or assay in PRIDE Inspector:

  • 1.

    Download, uncompress and open PRIDE Inspector
  • 2.

    Click in the magnifier on the left top corner, paste the project or assay that you would like to open in the search box, and hit search
  • 3.

    Click in the corresponding "Download" button to download the files and visualize them

Summary

Title

Preterm birth CVF proteomics discovery

Description

Preterm birth, defined as birth <37 weeks of gestation, is a leading cause of infant morbidity and mortality. In the United States, approximately 12% of all births are preterm.1 Despite decades of research, there has been little progress in developing effective interventions to prevent preterm birth. In fact, the rate of preterm birth has increased slightly over the last several decades.2 The ultimate goal of the Genomic and Proteomic Network for Preterm Birth Research (GPN-PBR) is to identify possible biomarkers that could predict the susceptibility to spontaneous preterm birth (SPTB) as well as to shed light on the molecular mechanisms involved in its etiologies. Understanding those mechanisms will help us predict SPTB and may facilitate the introduction of more effective prevention and treatment strategies.

Sample Processing Protocol

Proteins were precipitated using a standard methanol/chloroform protocol and digested with trypsin (Promega, Madison, WI). Samples were analyzed by microflow reversed phase LC-electrospray ionization/MS/MS using a high-resolution LTQ Orbitrap-XL instrument (Thermo Scientific, San Jose, CA) operating at a resolution of 100,000 at mass number/charge number 400.

Data Processing Protocol

Pproteins were precipitated using a standard methanol/chloroform protocol and digested with trypsin (Promega, Madison, WI). Samples were analyzed by microflow reversed phase LC-electrospray ionization/MS/MS using a high-resolution LTQ Orbitrap-XL instrument (Thermo Scientific, San Jose, CA) operating at a resolution of 100,000 at mass number/charge number 400. The MS/MS spectra were searched against an indexed human RefSeq database (version updated November 2007; 33,439 entries) with TurboSEQUEST (version 27.12; Thermo Scientific, Waltham, MA) and Mascot (version 2.2.03; Matrix Science, Boston, MA). Strict trypsin cleavage rules with maximum of 2 missed cleavages, mass accuracy of 1 Da for the precursor and fragment ion, and variable modifications of methionine oxidation, carboxyamidomethlyation on cysteine, [13C615N2]-lysine and [13C615N1]-leucine, were applied in the search criteria. The SEQUEST (Thermo Scientific) and Mascot (Matrix Science) output files were integrated into Scaffold (version 2.01; Proteome Software, Portland, OR) for validating MS/MS-based peptide and protein identifications. Assignment of peptide sequences was performed using the PeptideProphet algorithm.17 PeptideProphet accounts for the distribution of scores over an entire data set to calculate the probability of a correct assignment for every peptide. PeptideProphet calculates false-positive error rates at specific probability score cutoff values for each data set.18 A minimum PeptideProphet probability score of ≥0.5 was used to remove low probability peptides. At this cutoff, the estimated false-positive error rate was 10.8%. Protein identifications were accepted with a minimum ProteinProphet probability score of ≥0.8 and at least 2 identified unique peptides.19 For this dataset, a ProteinProphet probability score of ≥0.8 corresponded to a false-positive error rate of 4%. Proteins that contained similar peptides and could not be differentiated based on MS/MS analysis alone were grouped to satisfy the principles of parsimony.

Contact

Suhong Zhang, U Penn
Ian A Blair, U penn ( lab head )

Submission Date

26/08/2014

Publication Date

28/08/2014

Tissue

Not available

Cell Type

epithelial cell

Disease

disease free

Experiment Type

Shotgun proteomics

Assay count

6

Publication

    Parry S, Zhang H, Biggio J, Bukowski R, Varner M, Xu Y, Andrews WW, Saade GR, Esplin MS, Leite R, Ilekis J, Reddy UM, Sadovsky Y, Blair IA; Maternal serum serpin B7 is associated with early spontaneous preterm birth., Am J Obstet Gynecol, 2014 Jun 19, PubMed: 24954659

Assay

Showing 1 - 6 of 6 results
# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 39595 First Visit Preterm 1279 33818 2267 61864 15797
2 39599 First visit Control 958 25320 1807 49294 11081
3 39598 Second Visit Term 1216 30200 2119 63384 13842
4 39600 Second Visit preterm 1216 30200 2119 63384 13842
5 39597 Third Visit Term 857 34793 1949 67937 14915
6 39596 Third Visit preterm 1190 33118 2187 64669 14679