Hi everybody: I have a large proteomics LC-MS/MS dataset that I've generated on a Bruker Q-FTICR MS, and would like to run it through the TPP as I am successfully doing with my Orbitrap datasets.
I know I have a number of high quality hits (X!tandem expect values 1e-7, Mascot hits, same peptide in Orbi dataset, match with standard peptides) but I am either not getting data processed through TPP, or getting odd results--likely due to file conversion issues. For example: 1. Compassxport in line spectra mode (.baf->.mzxml) results in poor quality spectra and no IDs. 2. Compassxport in profile spectra mode (.baf ->.mzxml) crashes on my 10-20Gb input files. 3. Data Analysis export of .mgf files followed by X!Tandem followed by pep.xml conversion results in pep.xml files with visible X!tandem hits, but no probabilities produced by peptideprophet >0. Is there a reason peptide prophet cannot assign probability scores to pep.xml files generated from .mgf input? 4. Data Analysis export of .mgf conversion, perl script to .dta, perl script .dta to mzxml results in TPP results, however my final .mzxml files are scrambled with incorrect scan numbers. Obviously this is a complicated issue but any insight would be appreciated. Alternatively, does anyone know researchers running Bruker datasets in the TPP whom I could contact directly?. Thanks, -Chris -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
