Dataset Information

Analysis of lung cancer cell lines GLC1 and GLC1 M13

ABSTRACT: Datasets 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.

INSTRUMENT(S): Bruker Daltonics flex series, instrument model

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Gereon Poschmann

PROVIDER: PXD000132 | Pride | 2013-07-26

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	CTAB_SDS_PAGE.zip	Other
	IEF_SDS_PAGE.zip	Other
	PRIDE_Exp_Complete_Ac_28391.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_28391.pride.mztab.gz	Mztab
	PRIDE_Exp_Complete_Ac_28391.xml.gz	Xml

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Publications

A combination of two electrophoretical approaches for detailed proteome-based characterization of SCLC subtypes.

Poschmann Gereon G Lendzian Anna A Uszkoreit Julian J Eisenacher Martin M Borght Ann Vander AV Ramaekers Frans C FC Meyer Helmut Erich HE Stühler Kai K

Archives of physiology and biochemistry 20130508 3

<h4>Context</h4>Small cell lung cancers (SCLC) are heterogeneous and tumours differ in growth characteristics and treatment resistance.<h4>Objective</h4>To get insight into the underlying protein profiles responsible for this heterogeneity, two subtypes of SCLC cells mutually differing in chemo resistance properties and growth characteristics are analysed.<h4>Materials and methods</h4>Two different electrophoresis approaches in combination with mass spectrometry were used to detect differences b ...[more]

PMID: 23651173

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