PXD000214

PXD000214 is an original dataset announced via ProteomeXchange.

Title	Identification of Autocrine Growth Factors Secreted by CHO cells for Applications in Single Cell Cloning Media
Description	To identify low abundance autocrine growth factors in CHO cell conditioned media, we utilized a label-free shotgun proteomics approach. CHO cell conditioned media were harvested from fed batch bioreactors and concentrated using methanol/chlorofrom precipitation. Proteins in the samples were then subjected to proteolysis with trypsin, and then subjected to primary fractionation using a SCX column, followed by RP liquid chromatography MS (LC-MS) with a LTQ Orbitrap Velos instrument using the data dependent acquisition (DDA) method. The MS system was set up and run with a method which enabled fast acquisitions of high quality peptide precursor and fragment ion data, with the desired precursor mass accuracy of ±5 ppm. For the LTQ Orbitrap Velos MS, the data-dependent MS/MS analytical workflow in positive ion mode was used. Each precursor survey scan (m/z: 300 to 1800) by the Orbitrap mass analyzer (resolution = 60,000 FWHM) was linked to 10 MS/MS events using the 2D ion trap CID approach, with dynamic ion exclusion set at 60 s. This value was determined based on the observed mean peptide chromatographic peak width. All other instrument parameters were set up according to the manufacturer’s suggested values for complex peptide samples. The nano-ESI source was fitted with a 30-µm stainless steel nano-bore emitter (Thermo Fisher Scientific) with 1.7 kV applied near the tip. Raw data files from the LTQ Orbitrap Velos MS were processed using the Proteome Discoverer 1.3 software (Thermo Fisher Scientific). The LC-MS data were searched against the human (Homo sapiens; UniProtKb, updated in August 2012, 45 848 entries), mouse (Mus musculus; UniProtKb, updated in August 2012, 31 528 entries) and chinese hamster (Cricetulus griceus; UniprotKb, updated in August 2012, 24 609 entries) protein databases using the Sequest search engine for the LTQ Orbitrap Velos LC-MS data, assuming tryptic digestion with precursor ions to fall within 10 ppm of projected m/z values and a fragment ion mass tolerance of 0.5 m/z. The specified search parameters were carbamidomethylation of cysteine as fixed modification, oxidation of methionine as dynamic modification and a maximum of two missed cleavage events. Reverse database searching resulted in a specific false discovery rate (FDR) of 1% at the peptide and protein level.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:59:21.849.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	U MING LIM
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Cricetulus griseus (Chinese hamster) (Cricetulus barabensis griseus); NCBI TaxID: 10029; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2013-04-16 00:27:39	ID requested
1	2020-01-22 01:52:37	announced
⏵ 2	2024-10-22 04:59:26	announced	2024-10-22: Updated project metadata.

10.1021/pr400352n;

Lim UM, Yap MG, Lim YP, Goh LT, Ng SK, Identification of autocrine growth factors secreted by CHO cells for applications in single-cell cloning media. J Proteome Res, 12(7):3496-510(2013) [pubmed]

curator keyword: Biological

submitter keyword: Secreted Proteins,Chinese Hamster Ovary Cells, Shotgun Proteomics, Autocrine Growth Factors

Say Kong Ng
contact affiliation	Bioprocessing Technology Institute , Agency for Science, Technology and Research-A*STAR, 20 Biopolis Way 06-01, Singapore 138668, Republic of Singapore
contact email	ng_say_kong@bti.a-star.edu.sg
lab head
U MING LIM
contact affiliation	Mass Spectrometry
contact email	lim_u_ming@bti.a-star.edu.sg
dataset submitter

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/pride/data/archive/2020/01/PXD000214

PRIDE project URI

• PRIDE
  1. PXD000214
     1. Label: PRIDE project
     2. Name: Identification of Autocrine Growth Factors Secreted by CHO cells for Applications in Single Cell Cloning Media