PXD018127
PXD018127 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | MudPIT analysis of the proteins associated with FLAG-Hoxa1 and FLAG-Hoxb1 purified from chromatin fractions isolated from mouse KH2ES |
Description | MudPIT Analysis Four biological replicates of FLAG-Hoxa1, and corresponding negative controls, and FLAG-Hoxb1, and corresponding negative controls, were prepared from a chromatin enriched fraction isolated from mouse KH2ES cells and subjected to FLAG affinity purification. The eluted proteins were TCA-precipitated and analyzed by MudPIT. TCA-precipitated proteins were urea-denatured, reduced, alkylated and digested with endoproteinase Lys-C (Roche) followed by modified trypsin (Promega). Peptide mixtures were loaded onto 250 um fused silica microcapillary columns packed with strong cation exchange resin (Luna, Phenomenex) and 5-um C18 reverse phase (Aqua, Phenomenex), and then connected to a 100 um fused silica microcapillary column packed with 5-um C18 reverse phase (Aqua, Phenomenex). Loaded microcapillary columns were placed in-line with a Quaternary Agilent 1100 series HPLC pump and a LTQ linear ion trap mass spectrometer equipped with a nano-LC electrospray ionization source (ThermoScientific, San Jose, CA). Fully automated 10-step MudPIT runs were carried out on the electrosprayed peptides. Tandem mass (MS/MS) spectra were interpreted using ProluCID (v. 1.3.3) against a database consisting of 78014 nonredundant Mus musculus proteins (NCBI, 2016-06-23 release), 193 usual contaminants (human keratins, IgGs, and proteolytic enzymes). To estimate false discovery rates (FDR)s, the amino acid sequence of each non-redundant protein entry was randomized to generate a virtual library. This resulted in a total library of 116008 non-redundant sequences against which the spectra were matched. All cysteines were considered as fully carboxamidomethylated (+57 Da statically added), while methionine oxidation was searched as a differential modification. DTASelect (v. 1.9) and swallow, an in-house developed software, were used to filter ProLuCID search results at given FDRs at the spectrum, peptide, and protein levels. Here all controlled FDRs were less than 5%. All 16 data sets were contrasted against their merged data set, respectively, using Contrast v 1.9 and in house developed sandmartin v0.0.1. Our in-house developed software, NSAF7 v0.0.1, was used to generate spectral count-based label free quantitation results. |
HostingRepository | MassIVE |
AnnounceDate | 2020-10-20 |
AnnouncementXML | Submission_2020-10-20_13:24:02.xml |
DigitalObjectIdentifier | |
ReviewLevel | Non peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Ying |
SpeciesList | scientific name: Mus musculus; common name: house mouse; NCBI TaxID: 10090; |
ModificationList | S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide |
Instrument | LTQ |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2020-03-20 11:50:40 | ID requested | |
⏵ 1 | 2020-10-20 13:24:03 | announced |
Publication List
no publication |
Keyword List
submitter keyword: KH2 embryonic stem cells, Hoxa1, Hoxb1, FLAG affinity purification |
Contact List
Laurence Florens | |
---|---|
contact affiliation | The Stowers Institute for Medical Research |
contact email | laf@stowers.org |
lab head | |
Ying | |
contact affiliation | Stowers Institute |
contact email | yzh@stowers.org |
dataset submitter |
Full Dataset Link List
MassIVE dataset URI |
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://massive.ucsd.edu/MSV000085127/ |