Protocol: Marelli_protocol (LCMS2)

Name Marelli_protocol (LCMS2)
Description Prepare and run LCMS, producing one mzXml file per input sample.
Max input data per instance
Max input material per instance
Output data per instance
Output material per instance
Category mass_spec
TreatAsFractions false
ApplicationLSIDTemplate ${RunLSIDBase}:MS2.PreSearch
ApplicationNameTemplate Do MS2 Run
Material Inputs
Data Inputs
Material Outputs
Data Outputs
Protocol Steps
Step Name Description
1 Marelli_protocol (LCMS2) Prepare and run LCMS, producing one mzXml file per input sample.
10 Marelli_protocol Sample Prep An organellar 20KgP fraction was subjected to isopycnic density gradient centrifugation and analyzed by SDS-PAGE and Coomassie blue staining. Fractions enriched for peroxisomes (EP) or mitochondria (M) were identified by Western blotting. Equal amounts of protein derived from each of the hypotonically lysed M and EP fractions were combined and analyzed by ICAT MS/MS.
30 Marelli_protocol LC MS2 ICAT-labeled peptides were analyzed by µLC-ESI-MS/MS. Peptides were separated by on-line reversed-phase chromatography using a 75 µm x 10 cm self-packed Magic C18AQ column (Michrom BioResources) at a flow rate of 300 nL/min. Peptide fragmentation by collision-induced dissociation was performed in an automated fashion using the dynamic-exclusion option from the full-range MS spectra or by GPFm/z using an ion trap mass spectrometer (Thermofinnigan; Yi et al., 2002).
40 Convert to mzXML
1000 Mark Run Outputs