Project : PXD000226

View in PRIDE Inspector
Download Project Files

Summary

Title

Human Uterine Smooth Muscle S-nitrosoproteome

Description

S-nitrosoproteome of human unterine smooth muscle in different states of pregnancy (Labor, non labor, and preterm labor). Samples were isolated by the biotin switch and streptavidin pulldown before being analyzed by MS/MS on an Orbitrap instrument. Database Searching and bioinformatics: Tandem mass spectra were extracted; charge state deconvolution and deisotoping were not performed. All MS/MS samples were analyzed using Sequest (Thermo Fisher Scientific, San Jose, CA, version v.27, rev. 11). Sequest was initiated to search the database containing ipi.HUMAN.v3.87, the Global Proteome Machine cRAP v.2012.01.01, and random decoy sequences (183158 entries) assuming the digestion enzyme trypsin. Sequest was searched with a fragment ion mass tolerance of 1.00 Da and a parent ion tolerance of 10 ppm. Oxidation of methionine, iodoacetamide derivative of cysteine, and n-ethylmaleimide on cysteine were specified in Sequest as variable modifications. Criteria for Protein Identification-PROTEOIQ (V2.6, www.nusep.com) was used to validate MS/MS based peptide and protein identifications. Peptides were parsed before analysis with a minimum Xcorr value of 1.5 and a minimum length of 6 amino acids. There were no matches to the concatenated decoy database and therefore a false discovery value is not applicable or "0". Peptide identifications were accepted if they could be established at greater than 95.0% probability as specified by the Peptide Prophet algorithm. Protein identifications were accepted if they could be established at greater than 95.0% probability and contained at least two identified peptides with 5 spectra per peptide. Protein probabilities were assigned by the Protein Prophet algorithm. Proteins that contained similar peptides and could not be differentiated based on MS/MS analysis alone were grouped to satisfy the principles of parsimony.

Sample Processing Protocol

See details in reference PMID : 23948706

Data Processing Protocol

See details in reference PMID : 23948706

Contact

Craig Ulrich, Pharmacology

Submission Date

25/04/2013

Software

Unknown

Modification

Not available

Quantification

Not available

Experiment Type

Bottom-up proteomics

Assay count

9

Publication

    Ulrich C, Quilici DR, Schlauch KA, Buxton IL. The human uterine smooth muscle S-nitrosoproteome fingerprint in pregnancy, labor, and preterm labor. Am J Physiol Cell Physiol. 2013 Oct 15;305(8):C803-16 PubMed(s) : 23948706

Assay

Accession Title Protein Count Peptide Count Unique Peptide Count Spectrum Count Identified Spectrum Count
29476 Craig 1943 7534 2562 8128 7534
29477 Craig 1885 6976 2485 7547 6976
29478 Craig L3 2092 7105 2688 7716 7105
29479 Craig NL2 1811 7184 2425 7828 7184
29480 Craig NEM NL3 2068 7235 2665 7770 7235
29481 Craig NEM 2054 6711 2613 7279 6711
29482 Craig NEM 1692 5734 2069 6069 5734
29483 Craig NEM 2281 7291 2855 7816 7291
29484 Craig NEM 1954 7156 2565 7812 7156

You are about to run PRIDE Inspector via Java Web Start. Double click on the JNLP file downloaded if it didn't start automatically.

Note: Due to Oracle's recent Java update, you may experience security related problems with Java Web Start. Please add "http://www.ebi.ac.uk" to the URLs listed in the Security tab of your Java Control Panel.