Skip to main content

Topic: Conversion from .RAW to mzXML and then export specific scans as .txt (Read 443 times) previous topic - next topic

  • MKnight
  • [*]
Conversion from .RAW to mzXML and then export specific scans as .txt
Hi all,

I am currently in the process of doing some data analysis for some MS/MS work I have been doing. I am planning to use SIRIUS (https://bio.informatik.uni-jena.de/software/sirius/) for molecular formula elucidation and structure prediction. SIRIUS needs centroided data, however, and unfortunately my MS2 analysis was all accrued out in profile mode. Additionally, the version of Xcalibur I used was several versions out of date (SP 2.2, rather than 2.9), so there . I understand that converting from .RAW to mzXML also converts the spectrum to centroid, but I have yet to find a software that then allows me to open .mzXML files and interact with the spectra, including exporting specific scans as .csv or .txt files. I need the raw data as text so that I can write my own .mgf files which contain the relevant information per energy level. I have tried software such as OpenMS and ProteoWizard, both of which seem to allow me to view spectra, but not exports the scans I am interested in. Could anyone suggest a free software that would allow me to do this?

Thanks a lot!
  • Northumbria University

  • sneumann
  • [*][*][*]
Re: Conversion from .RAW to mzXML and then export specific scans as .txt
Reply #1
Hi, in pwiz you have the mscat command line tool, in R you can use mzR for reading raw mz* data,
and/or MSnbase for a higher-level interface. Yours, Steffen
--
IPB Halle                          Mass spectrometry & Bioinformatics
Dr. Steffen Neumann         http://www.IPB-Halle.DE
Weinberg 3 06120 Halle     Tel. +49 (0) 345 5582 - 1470
sneumann(at)IPB-Halle.DE