Project PXD000226

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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

Publication Date

02/03/2014

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

Showing 1 - 9 of 9 results
# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 29476 Craig 1943 7534 2562 8128 7534
2 29477 Craig 1885 6976 2485 7547 6976
3 29478 Craig L3 2092 7105 2688 7716 7105
4 29479 Craig NL2 1811 7184 2425 7828 7184
5 29480 Craig NEM NL3 2068 7235 2665 7770 7235
6 29481 Craig NEM 2054 6711 2613 7279 6711
7 29482 Craig NEM 1692 5734 2069 6069 5734
8 29483 Craig NEM 2281 7291 2855 7816 7291
9 29484 Craig NEM 1954 7156 2565 7812 7156