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DTSTAMP:20260710T141511Z
UID:a60410d5-5137-467a-b1f5-1418b7d28dba
DTSTART:20251217T080000Z
DTEND:20251217T120000Z
DESCRIPTION:Educator:\nDavid L. Tabb (CIBI)\n\nDate:\nDecember 17\, 2025 9:
 00 AM-noon\n\nLocation:\nUniversity of Antwerp\n\nContents:\nThis course t
 eaches the use of FragPipe and FragPipe Analyst to identify and quantify D
 DA and DIA proteomes\, seeking differential protein expression.\n\nProteom
 ics technologies such as LC-MS/MS (liquid chromatography coupled with tand
 em mass spectrometry) are a natural fit for clinical biology because these
  technologies powerfully detect changes in protein concentration and modif
 ication.  This hands-on training will introduce the key steps required to 
 quantify and differentiate proteins\, matching tandem mass spectra to pote
 ntial peptide sequences and inferring proteins from them\, integrating chr
 omatograms to estimate quantities for peptides and proteins\, and statisti
 cally testing for differences in protein quantities between two cohorts.\n
 \nThis study will use data from PXD044981 (https://doi.org/10.1021/acs.jpr
 oteome.4c00048)\, which applied both DDA (the classic LC-MS/MS identificat
 ion technique) and DIA (a method intended to quantify thousands of peptide
 s at once) to measure a yeast background with human proteins spiked at dif
 ferent quantities.  Dr. Tabb will guide the participants through the proce
 ss of identifying and quantifying these data sets in FragPipe (https://fra
 gpipe.nesvilab.org/)\, followed by statistics and visualization in the Fra
 gPipe Analyst web interface.\n\nLearning goals:\nParticipants should gain 
 the ability to use the LFQ-MBR (label-free quantitation\, match-between-ru
 ns) and DIA_SpecLib_Quant workflows in FragPipe 23.1.  They will be able t
 o pass the results of these analyses to the FragPipe Analyst website for d
 etecting differential protein expression.\n\nPrerequisites:\nParticipants 
 should bring laptops to be able to carry out this training on their own co
 mputers\; for best results\, we suggest that the computers feature at leas
 t 8GB of RAM.  FragPipe can be used in Microsoft Windows and Linux.  Prior
  to the training\, we recommend that students try to install FragPipe on t
 heir laptops in case they need administrator passwords for this process.\n
 \nKeywords:\nProteomics\, Bioinformatics\, LC-MS/MS\, MSFragger\, FragPipe
 \, biomarkers\n\nTools:\nFragPipe\, MSFragger\, FragPipe Analyst
SUMMARY:Differential Proteomics Training
URL;VALUE=URI:https://www.denbi.de/training-courses-2025/2002-differential-
 proteomics-training
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