Proteomics

Dataset Information

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Concentration determination of >200 proteins in dried blood spots for biomarker discovery and validation


ABSTRACT: Raw files were created using XCalibur 3.0.63 (Thermo Scientific) software and analysed with Thermo Proteome Discoverer 2.2.0.388 software suite (Thermo Scientific). The raw data files were processed as previously described 26 with the following modifications: the peak lists were submitted to Mascot 2.4.1and Sequest servers using the UniProt human database 28 which contained 20,338 protein sequences. The enzyme was set to Trypsin (Full) with max missed cleavage set to 2. The fixed modification was set to carbamidomethyl and variable modifications were set as oxidation (M), deamidation (NQ), and N-terminal methionine loss. Precursor and fragment mass tolerances were set at 8 ppm and 0.8 Da, respectively. Peptide spectral match validation was performed using Percolator setting the maximum Delta Cn to 0.05 and decoy database searches at 0.01 for target FDR (Strict), 0.05 (relaxed) and validation based on q-Value

INSTRUMENT(S): Orbitrap Fusion

SUBMITTER: Christoph H. Borchers  

PROVIDER: MSV000084629 | MassIVE | Wed Nov 27 09:57:00 GMT 2019

SECONDARY ACCESSION(S): PXD016484

REPOSITORIES: MassIVE

Dataset's files

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params.xml Xml
20170305DBSA.mzXML Mzxml
20170305DBSSTDA.mzXML Mzxml
20170305DBSA.raw Raw
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Publications

Concentration Determination of >200 Proteins in Dried Blood Spots for Biomarker Discovery and Validation.

Eshghi Azad A   Pistawka Adam J AJ   Liu Jun J   Chen Michael M   Sinclair Nicholas J T NJT   Hardie Darryl B DB   Elliott Monica M   Chen Lei L   Newman Rachael R   Mohammed Yassene Y   Borchers Christoph H CH  

Molecular & cellular proteomics : MCP 20200102 3


The use of protein biomarkers as surrogates for clinical endpoints requires extensive multilevel validation including development of robust and sensitive assays for precise measurement of protein concentration. Multiple reaction monitoring (MRM) is a well-established mass-spectrometric method that can be used for reproducible protein-concentration measurements in biological specimens collected via microsampling. The dried blood spot (DBS) microsampling technique can be performed non-invasively w  ...[more]

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