Skyline for small molecules/metabolomics and Skyline 20.1!

Skyline has had support for small molecules and metabolites for years now-- but I still have a lot of trouble setting it up and have to bug smarter (and typically younger...) people for help a lot.  What I could use is a Step-by-Step protocol and template files I can download. 

--- and here it is! 

While I'm on the Skyline topic -- I just got this great email overnight -- Skyline 20.1 is up. 

It does require a manual download and install (which you can download here) -- but the Skyline team hasn't forgotten about proteomics.

Edit: On my laptop that has the Windows 10 disease, I did have to manually remove the last install of Skyline and reboot to install 20.1.

I've trimmed the email to remove any mention of command line Skyline and stats words I'm unfamiliar with. And highlighted my favorite parts. 

MSFragger spectral libraries!! Pull out the dark proteome and then quantify it?!?  For the biopharma groups that are finding multi attribute monitoring the most cost-effective way forward? Supported! 

Improvements since Skyline 19.1 include:

• Prosit spectrum and iRT prediction support directly integrated into the UI
  • Building libraries for targeted peptides in a document through Peptide Settings - Library - Build button.
  • Prosit spectrum prediction viewing in the Spectrum Match plot with new right-click menus, including mirror plotting
  • Settings in Tools > Options > Prosit
• Support for spectral library building from MS Fragger pepXML search results
• Support for diaPASEF!
  • We have run this with 2 separate 3-organism datasets through the LFQBench statistical assessment and that works.
• Improved ddaPASEF and initial prmPASEF support.
• Performance gains in importing Agilent and Waters IMS data as much as 2x or more.
• Parallel file import with proteomewide DIA in the UI or by default on the command-line has performance similar to what was previously only available from the command-line using --import-process-count. Choose "Many" on your next import or just ignore threading the next time you import from the command-line.
• Optimized spectrum memory handling for instrument vendors with .NET data reader libraries, benefitting Agilent, SCIEX, and Thermo
• A new "Consistency" tab in the Refine > Advanced form, supporting CV and q value cut-offs
• New checkbox for Refine > Advanced - Results tab Max precursor peak only
• Support for Multiple Attribute Model (MAM) grouping with Peptide.AttributeGroupID and PeptideResults.AttrributeAreaProportion
• Added File.SampleID and .SerialNumber (of the instrument) as fields in Document Grid custom reports
• Transitions Settings - Full-Scan - MS/MS filtering has been extended to apply to all non-MS1 spectra (e.g. MS3) as long as the MS1-level precursor matches the target precursor m/z The redundant library filtering phase of spectral library building is around 20x
• Improved iRT calibration UI making it easy to create new sets of standards based on existing sets that can be used in spectral library building and the Import Peptide Search wizard
• More iRT improvements including more intelligent use of 80+ CiRT peptides when CiRT is chosen during library building
• New right-click > Quantitative menu item for changing the Quantitative property on transitions in the Targets view TIC and BPC now come from raw data files and do not need to be extracted from MS1 spectra which has performance benefits for MS1 filtering
• New global "QC" transitions have been added such as the pressure trace
• Calibration curve fixes to make ImCal (Isotopolog Calibration Curves) work
• New "Calculated" annotations have been added which support storing Skyline calculated values in annotations for future use with AutoQC
• Support KEGG IDs as molecular identifiers in small molecule targets.
• Improved support for D used in chemical formulae in place of the Skyline default H'
• Added support for Thermo Exploris and Eclipse instruments
• Support for opening .skyp files downloaded directly from Panorama