I have used the X!tandem software for proteomics data search and couldn't get the correct output for my current settings below.
Residue modifications-> 144.1021@K
Residue potential modificatios->144.102063@Y
Oxidized M-> 15.9949@M
I want to find the correct setting for peptide N-terminus and Lysine residues as static modifications and oxidation of methionine as variable modification.
Further I couldn't find any place to put precursor mass range as well.
Thank You.
Dear Sugandima,
I can recommend you to use SearchGUI. It has a very nice graphical user interface to set the parameters. It runs multiple search engines (which you could deselect), including X!Tandem. It has a lot of features that can help you set the correct modifications without having to fiddle too much with command line parameters and XML files. You can find it at https://code.google.com/p/searchgui/. You can find the publication here: http://www.ncbi.nlm.nih.gov/pubmed/21337703.
Cheers !
It's best not to edit "default_input.xml"; instead, create parameters files for each search that link to the default settings. The reason for this approach is that the parameters files will be easy to read and manage since only the most important settings are included. I've attached an input file that I used recently, which includes things specific to my system (file paths; computational threads count) and work (protein sequence database name; iodoacetamide treatment; settings for precursor and fragment ion tolerances), but it covers the items you mention.
I like SearchGUI and its companion data browser, PeptideShaker. However, alternative pipelines that include X! Tandem are available. For iTRAQ data, I'd recommend the Trans-Proteomic Pipeline. It's harder to use than SearchGUI, but it incorporates a very good data browser.
Hi David,
Thank you so much. This was what I exactly looking for. Hope this is for iTRAQ-4plex. But I think I don't need Carbamidomethyl modification (+57.021464@C).
Yes, the numbers are for 4-plex iTRAQ and, yes, you should delete, "+57.021464@C," for carbamidomethylation.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools