[spctools-discuss] using XTandem native scoring with PeptideProphet

Hi, I use xtandem with native scoring and also TPP 4.4.1 The Tandem2XML converted .pep.xml file has: However, PeptideProphet complains about it: Error: The X! Tandem scoring algorithm 'tandem' is not supported. It will go through if I change it to read"native" in the .pep.xml file. I am wonde

Re: [spctools-discuss] XPRESS wrongly assigns "heavy" and "light" for some peptides

Oliver, If you can make a dataset available (ideally a single raw file in xml format and corresponding pep.xml), I can take a look. - Jimmy On Tue, Sep 6, 2011 at 5:11 AM, oschill...@gmail.com wrote: > Dear all, > > in some cases, XPRESS wrongly assigns "heavy" and "light" states for > some pep

Re: [spctools-discuss] Does mzML(converted from RAW), WIFF, MGF, DTA, and pepXML contains "mono-isotopic mass weight Information"?

In addition to Gavin's comments, I can answer for mzML and msconvert specifically. MzML has two places to put "precursor m/z", either the "isolation target m/z" in the isolationWindow element or the "selected ion m/z" in a selectedIon element. On the Thermo Orbi or FT, the trigger mass is usual

[spctools-discuss] SPC devs incommunicado

I'm forwarding this on behalf of Eric: Hi everyone, for those of you wondering why the list has been so quiet, our Google email accounts have all been changed on us in a way that prevents us from replying and moderating our own group. We are also traveling in Geneva which is making fixing the

[spctools-discuss] Thermo RAW metadata with msfilereader

Hi folks I am interested in extracting some metadata from our Thermo RAW files such as injection time and spray voltage for each scan in the file. I learned that deploying a program that interfaces with the msfilereader would be the easiest way to get the job done. I was wondering if someone has wr

[spctools-discuss] No probabilities after running peptide prophet with MALDI option

Hi everyone, I searched a MALDI dataset with Mascot and converted the results to pep.xml with Mascot2XML. Running peptide prophet on this dataset with the MALDI option set leads to no reported probabilities. However, when I uncheck the MALDI option, probabilities are reported. I tried various comb

[spctools-discuss] XPRESS wrongly assigns "heavy" and "light" for some peptides

Dear all, in some cases, XPRESS wrongly assigns "heavy" and "light" states for some peptides. This results of course in inverted, wrong ratios. "heavy" and "light" are correctly assigned by ASAP and verified by checking with Pep3d. We are using differential formaldehyde labeling. This problem occu