Skyline now has MS1 and full scan MS/MS analysis capabilities

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Skyline now has MS1 and full scan MS/MS analysis capabilities

Postby maccoss » Tue Aug 16, 2011 12:10 pm

The popular Skyline Targeted Proteomics Software environment was updated at ASMS with a number of new capabilities.

Skyline v1.1 Released on 6/11/11

New features include:

  • Import results from WIFF files much improved (50-fold faster for large scheduled runs - thanks to AB SCIEX)
  • Full-scan MS/MS ion chromatogram extraction
  • Full-scan MS1 multiple isotope ion chromatogram extraction
  • Full-scan method export for Thermo LTQ
  • Import document with multiple documents and support for merging results
  • Integrated support for Unimod modification definitions
  • Modification auto-detect support for pasted/inserted annotated peptide sequences
  • Native method export for AB SCIEX QTRAP
  • Native method export for Agilent 6400 Series
  • Spectral library build support for Scaffold, Waters MS^e and OMSSA
  • Improved Edit / Find in the Peptide View
  • Larger text sizes in the peptide tree view
  • Multi-select annotation editing
  • Multiple color annotation indicators
  • Improved scheduling for multi-replicate documents
  • Variable modification and neutral loss detection in transition list paste/insert/import
  • Peptide filter expression support for matching modifications
  • New bulk refinement operations
  • Replicate acquired time in reports and replicate plot ordering
  • New summary plots

We are working hard on Skyline v1.2 and new features will include:

  • Command-line interface for running Skyline operations in automated scripts on instrument control computers
  • New isotope dot-product score on MS1 full-scan filtered peaks, and expected relative isotope abundance in peak area plot and reports
  • Modification auto-detect for the Spectral Library Explorer
  • Faster MS/MS library loading
  • Improved memory performance for full-scan chromatogram extraction
  • Improved full-scan method export for Thermo LTQs, including support for Accurate Inclusion Mass Spectrometry (AIMS)
  • New enhanced Find with Find All
  • Unexpected error form with button to report the issue

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E. Coli Lysate Member
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Postby Doug » Wed Feb 15, 2012 6:08 pm

Skyline v1.2 was released today from Brendan MacLean and other from the MacCoss lab in Seattle. More info here.

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Postby shanyichu » Tue Dec 24, 2013 6:30 pm

I have some problems when using Skyline for MS1 based quantification.
(1)I install skyline on different computers. it works on one computer, but for another computer, everything is fine before importing the results.
but when i import the results, a message showed up "please add at least one target transition before importing results". The two computers are very similar, I don't know why this happen?
(2) for the ms1 peak area calculated by skyline, I found that there is only the area for each peptide, but not for the modified peptide.
In other words, the modification information doesn't exist in the output files. So if one peptides has different forms of modification, i. e.
with M oxidation and without M oxidation, what is the peak area? does skyline merge all area of different forms of one peptide?
(3) i want to deal with a lot of wiff files and group files because I run two-dimensional chromatography. How can I do the quantification in batch? By now I have to finish quantification for one file, and then do another.
Thanks a lot in advance!

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