Hi all, I am comparing XPress peptide results between TPP versions *4.1* and *4.6*. Given the same input pep.xml file and mzXML file, the results from the two versions are quite different (R-squared of ~0.3). To my surprise, the 4.1 results seem much better. Let me provide some details, and maybe someone can help me improve my results.
*Version and Parameters* TPP 4.1 <xpressratio_summary version="2.1 (TPP v4.1 JETSTREAM (RC) rev 0, Build 200806181121 (linux))" author="Jimmy Eng" same_scan_range="Y" labeled_residues="Kn" xpress_light="1" massdiff="K,8.04 n,8.04" masstol="0.02"/> TPP 4.6 <xpressratio_summary version="2.1 (TPP v4.6 OCCUPY rev 3, Build 201308191103 (linux))" author="Jimmy Eng" same_scan_range="Y" labeled_residues="Kn" xpress_light="1" massdiff="K,8.044370 n,8.044370" masstol="0.020000" ppmtol="0" min_num_chromatogram_points="6" min_num_isotope_peaks="0"/> *Specific Result* *pep.xml input:* scan: 1576 precursor_neutral_mass: 2492.1902 assumed_charge: 3 retention_time_sec: 1771.0 peptide: GQKSPGALETPSAAGSQGNTASQGK calc_neutral_pep_mass: 2492.1908 massdiff: -0.000630 mod_nterm_mass: 29.039125 mod_aminoacid_mass - position 3, mass 156.126263 - position 4, mass 166.998358 - position 25, mass 156.126263 *TPP 4.1 xpressratio result:* light: scans 1555-1604, mass 2493.199, area 3.13e+06 heavy: scans 1555-1604, mass 2517.332, area: 3.43e+06 decimal_ratio: 0.91 *TPP 4.6 xpressratio result:* light: scans 1524-1649, mass 2493.1981, area 3.19e+06 heavy: scans 1524-1644, mass 2517.3312, area: 3.43e+06 decimal_ratio: 0.93 *Notes:* - The 4.1 light mass is 1.008 Da greater than the peptide neutral mass, and the 4.6 light mass is 1.0073 Da greater. In this regard, I believe *version 4.6 is correct*, because the light mass equals the neutral mass plus the mass of a proton (rather than the mass of hydrogen). - The 4.6 result has a very wide scan window. In this regard, the *4.1 result seems correct*. The image below is an extracted ion chromatogram, with the 4.6 result width. On the other hand, the 4.1 result starts and stops where you would expect, around 19.25s - 29.75s. <https://lh6.googleusercontent.com/-kyql1liKr5k/UqJXaoatn0I/AAAAAAAAAIQ/Yysv4stwVJA/s1600/1576.xic.png> *Comparison* The first scatter plot (n=197) shows log2 ratios for the two versions, with a poor correlation. The second two plots show the xpress ratios vs MasschroQ ratios for confirmation. You can see that the old TPP 4.1 results correlate much better with MassChroQ. <https://lh4.googleusercontent.com/-ak_V4WFznps/UqYxM0Iu-LI/AAAAAAAAAIg/h4TFkCe_uOw/s1600/xpress_oldvnew.png> <https://lh3.googleusercontent.com/-JCh0394YMf8/UqYxTpJa2mI/AAAAAAAAAIo/td4xnbyYAno/s1600/xpress_mcqvold.png> <https://lh5.googleusercontent.com/-mH9zEfFJwf0/UqYxaHxSbLI/AAAAAAAAAIw/7RjADenxX2E/s1600/xpress_mcqvnew.png> *Summary* There seem to be changes in xpress between TPP 4.1 and 4.6, despite the version number remaining the same, which result in significantly different quantification. - Is there a changelog for xpress? - Am I correct about light and heavy mass calculations? When did those change? - How can I improve the peak start/end scans in the current (TPP 4.6) version of xpress so that they are not so wide? - Has any one else found that xpress quantifications have become seemingly *less* accurate in recent versions? Are there important new parameters that I need to tweak, or some other change that is necessary with the new version to improve my results? - If I were to revert to a previous version of xpress, should I revert all the way to 4.1, or is there an intermediate version that would be preferable? Thanks so much, and let me know if there is anything else useful that I can provide Jeff -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
