<<< Full experiment listing

PXD000132

PXD000132 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleAnalysis of lung cancer cell lines GLC1 and GLC1 M13
DescriptionDatasets contain protein identification and raw data from MALDI protein identifications. Identified proteins resulted from a comparison of GLC1 and GLC1 SCLC cell lines using 2D DIGE. MALDI-TOF-MS analyses were performed on an UltraFlexTM II (Bruker Daltonics) instrument according to the instructions of the manufacturer. The instrument was equipped with a scoutTM MTP MALDI target. The spectra were acquired in the positive ion mode according to the settings given by the manufacturer. For external calibration, a peptide standard (m/z 757.399, 1296.684, 1619.822, 2093.086 and 3147.471) was used. The MALDI-PMF spectra were processed using the FlexAnalysis™ 2.4 software (Bruker Daltonics) and converted in the .xml format. For peak detection, the spectra were subjected to an internal recalibration using 13 different monoisotopic masses from autolysis products of trypsin and fragments of keratins ranging from m/z 842.509 – 2825.406. Following parameters were applied: snap peak detection algorithm, signal to noise threshold of 6, maximal number of peaks 100, quality factor threshold 50 and baseline subtraction TopHat. The generated mass lists were subsequently sent to ProteinScapeTM 1.3 (Bruker Daltonics, Bremen, Germany), triggering database searches using ProFound (Version 2002.03.01, Proteometrics LLC) and MASCOT (Version 2.3.02, Matrix Science, London, UK). The following search parameters were selected: fixed cysteine modification with propionamide, variable modification due to methionine oxidation, one maximal missed cleavage sites in case of incomplete trypsin hydrolysis and no details about 2-DE derived protein mass and pI. Using the Score booster function of ProteinScapeTM the mass lists were recalibrated and background masses removed using a list containing 44 masses occurring in a minimum of 10% of generated peak lists. The database searches were run with a mass tolerance of 40 ppm using UniProt’s human complete proteome set (downloaded on 26.10.2012) containing 68.109 protein entries. The used database is a composite database consisting of the UniProtKB entries and a duplicate of the same database, in which the amino acid sequence of each protein entry was randomly shuffled. Proteins reaching Profound score > 1.5 or Mascot score > 64 were considered as identified. Using these criteria one decoy database entry was found by the search engines indicating high confidence of protein identifications. If several database entries of homologues proteins matched these criteria only the entry with the highest score was reported.
HostingRepositoryPRIDE
AnnounceDate2013-05-08
AnnouncementXMLSubmission_2013-07-26_05:37:48.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD000132
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterGereon Poschmann
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo applicable mass modifications
Instrumentultraflex TOF/TOF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02013-01-24 04:06:45ID requested
12013-07-26 03:59:33announced
12014-07-28 00:29:12announced
22013-07-26 04:00:47announcedmissing
32013-07-26 05:36:57announcedmissing
42013-07-26 05:37:48announcedmissing
Publication List
Poschmann G, Lendzian A, Uszkoreit J, Eisenacher M, Borght AV, Ramaekers FC, Meyer HE, St, ü, hler K, A combination of two electrophoretical approaches for detailed proteome-based characterization of SCLC subtypes. Arch Physiol Biochem, 119(3):114-25(2013) [pubmed]
Keyword List
submitter keyword: SCLC, MALDI, classic and variant, cancer
Contact List
Gereon Poschmann
contact affiliationMolecular Proteomics Laboratory
contact emailgereon.poschmann@hhu.de
Full Dataset Link List
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://ftp.pride.ebi.ac.uk/2013/05/PXD000132
Repository Record List
[ + ]