Metadata |
datasetIdentifier | PASS00724 |
datasetType | SWATH |
submitter | Sarah Parker <sarah.parker@cshs.org> |
submitter_organization | Cedars-Sinai Medical Center |
lab_head_full_name | Jennifer van Eyk |
lab_head_email | Jennifer.VanEyk@cshs.org |
lab_head_organization | Cedars Sinai Medical Center |
lab_head_country | Unitest States |
datasetTag | CiRT_DIA_2015 |
datasetTitle | Raw DIA files and libraries used in the manuscript "Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-Independent Acquisition Mass Spectrometry" |
publicReleaseDate | 2015-08-30 00:00:00 |
finalizedDate | 2015-07-21 15:18:51 |
summary | Data independent acquisition files and corresponding library files used to demonstrate the value of a set of conserved, commonly occurring peptide sequences to align chromatographic retention time between spectral libraries and DIA files. |
contributors | Sarah J Parker, Hannes Rost, George Rosenberger, Ben C Collins, Lars Malmström, Dario Amodei, Vidya Venkatraman, Koen Raedschelders,Jennifer E Van Eyk, Ruedi Aebersold |
publication | Sarah J Parker, Hannes Rost, George Rosenberger, Ben C Collins, Lars Malmström, Dario Amodei, Vidya Venkatraman, Koen Raedschelders, Jennifer E Van Eyk, Ruedi Aebersold. Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-Independent Acquisition Mass Spectrometry, Molecular and Cellular Proteomics, Accepted July 2015 |
growth | |
treatment | |
extraction | Protein samples were lysed/extracted in 8M UREA |
separation | In some samples for DDA library building, peptides were fractionated by either basic reverse phase or OFFGEL to increase analytical depth. |
digestion | Trypsin |
acquisition | C18 reverse phase LC upstream of TripleTOF operating in either DDA mode (top 20 most intense ions fragmented) of DIA mode (25 x 32Da fixed windows with 0.5da overlap on each end). |
informatics | Peptide spectral matches from DDA data were made using !XTandem and probability scores assigned using peptide prophet. Spectral libraries were assembled in SpectraST (TPP v4.6), retention time aligned using custom python script spectrast2spectrast_irt.py and assay libraries generated using the custom python script spectrast2tsv.py with subsequent conversion to .TraML format and appending of Decoy peak groups in openMS. Targeted peak group extraction and scoring in DIA files was performed by openSWATH, with FDR modeling by pyprophet. |
instruments | SCIEX TripleTOF 5600 |
species | Human, Mouse, Yeast |
massModifications | static: C+57.021464, M+15.994915,S+79.966331, T+79.966331,Y+79.966331 |