| Metadata |
| datasetIdentifier | PASS00852 |
| datasetType | SRM |
| submitter | Sofia Waldemarson <sofia.waldemarson@immun.lth.se> |
| submitter_organization | Immunotechnology Lund University |
| lab_head_full_name | Peter James |
| lab_head_email | peter.james@immun.lth.se |
| lab_head_organization | Immunotechnology Lund University |
| lab_head_country | Sweden |
| datasetTag | AFFIRM_in-solution |
| datasetTitle | On-bead and in-solution protein capture in the AFFIRM immunoaffinity SRM assay format provide targeted protein analysis with high sensitivity from complex samples |
| publicReleaseDate | 2016-12-01 00:00:00 |
| finalizedDate | 2016-03-29 10:36:45 |
| summary | This dataset describes the use of biotin-tagged scFv and streptavidin coated magnetic beads for targeted protein captures in the immunoaffinity SRM platform AFFIRM. Proteins are captured using two setups, either incubating scFv and protein in-solution and after binding adding magnetic beads, or by incubating bead-coupled scFv in solution with target protein. Proteins are digested on-bead and analyzed with a peptide SRM readout. Dilution curves of target proteins in serum background from 1-125 ng/ml concentrations are analyzed. |
| contributors | Daniel Corbee, Anna Säll, Sara Vikström, Helena Persson, Sofia Waldemarson |
| publication | Corbee D, Säll A, Vikström S, Persson H, Waldemarson S - submitted |
| growth | Not applicable |
| treatment | This dataset is the analysis of recombinant human proteins spiked into a serum background at 1-125 ng/ml concentrations. Proteins are captured using scFv and magnetic beads, washed and on-bead digested for peptide SRM readout. |
| extraction | Not applicable |
| separation | Peptides are separated using and online HPLC-setup before entering the mass spectrometer. |
| digestion | Proteins are digested directly while retained on the magnetic beads by the scFv. Trypsin solution in ambic is used, no reduction and alkylation is performed. |
| acquisition | A transition list containing 31 peptides with 140 transitions was used and peptides analyzed on a triple stage quadropole mass spectrometer (TSQ Vantage, San José, CA, USA) operated in SRM mode at unit resolution (Q1, Q3) with 10 ms dwell time and 5 ms interscan delay. |
| informatics | Data acquisition was done using Xcalibur software (version 2.1). Raw data has been converted to mzML format using the Proteios software and the mzML files were used for analysis in Skyline. |
| instruments | TSQ Vantage |
| species | Human |
| massModifications | none |
