Chris, FWIW, we took a similar file format conversion path for Bruker data, but unfortunately I don't have experience with the X!Tandem/TPP issues.
The processing path we took was: - Data Analysis export of XML file (centroided "line" MS2 spectra), followed by perl script conversion to .dta (the XML format contains some metadata like compound indexes for each scan that was useful for downstream processing). - The .dta files were submitted to Sequest and Mascot, giving the expected search results. For your #4, do you know if the .dta to mzXML converter you are using expect a specific .dta file name format like <sample>.<first scan>.<last scan>.<charge>.dta? If so, and your .dta file names are different than this format, perhaps that is contributing to the scrambled/incorrect scan numbers in the generated mzZML. Andrew. On Jan 13, 7:30 pm, Chris Rath <[email protected]> wrote: > 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.
