Hi RawProt, Mono-isotopic is really dependant on the instrument rather than the file type. Instruments which provide a more accurate mass will give you a more reliable mono-isotopic mass.
For example, on a quadrupole instrument hydorxy-l-proline and leucine will probably give the same mass (132.1 m/z) for the H+ ion so this is not monoisotopic, whereas an Orbitrap will give you a more accurate mass and hence a monoisotopic mass. Of course, when the instrument is combined with some chromatography it is easier to identify analytes based on both their mass and retention time, but to provide a true mono-isotopic mass you need a capable instrument. As far as I'm aware, converting from proprietary file format (.RAW, .WIFF etc.) to mzML or mzXML retains all of the information contained within the original file but sets it out in a standard format. Others on here will be able to give a better answer. Cheers, Gavin. -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of RawProt Sent: 03 September 2011 21:29 To: spctools-discuss Subject: [spctools-discuss] Does mzML(converted from RAW), WIFF, MGF, DTA, and pepXML contains "mono-isotopic mass weight Information"? Hi Experts, I am somehow lost in the beginning phase of my first project in the Proteomics department. My main task: "Designing DATABASE" of various "FILE" formats existed in the Proteomics research (RAW, wiff, MGF, pepXML, dta). Till now main file formats are RAW, WIFF, MGF & DTA which are not in XML and XML based: pepXM. Obviously there is overlap in information in multiple different data file formats/experimental. Though analysis can be made from single file (experimental measurements) or by comparison between “sets of files”. But, what is missing? Understanding the re-occurring pattern in and between experiments. Of course “Database” is needed in querying experiments/(files) with varied parameters. That’s why file based searching is not efficient to our answer our question. What kind of "search term" in an experiments? "Mono-isotopic mass". "Have we seen this mono isotopic mass before in other experiments is the main issue in our research"? I have started to work with RAW-> mzML (convert). I went through the documentation of mzML available in the HUPO trying to design relational schema from mzML schema manually. Though mzML is quite well documented I have confess not being clear. Questions -------------- 1) Where information like*"mono isotopic mass"* are recorded in the mzML file? Is it precursor charge attribute in the spectrum Element? Or am I missing something? 2) Can I be sure that all RAW and mzML after conversion regardless of different vendors consists of "mono-isotopic mass" info? 3) Further, I am wondering does all mentioned files (wiff, pepXML,dta,mgf) too contains "mono-isotopic mass" information? 4) If all files doesn't contain "mono-isotopic mass" info, then what are the most distinct term? Please guide me! Regards, RawProt -- 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. -- 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.
