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Newsletter Archive

  • Newsletter 12 - Spring 2015 : Volume 7, Issue 1
  • Come see us this year at ABRF, MSACL, ASMS and Metabolomics 2015. Scaffold has been updated to support more file formats including AB SCIEX Protein Pilot 5.0, Agilent Spectrum Mill mzXML and more. The Quantify View has been enhanced with multiple features including a Volcano Plot. Scaffold perSPECtives has new features including FDR thresholding and protein grouping during loading, allowing users to set default parameters. Learn more about Elements for Metabolomics. We will be giving demos of this new product, now in beta testing.
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  • Newsletter 11 - Summer 2014 : Volume 6, Issue 2
  • Come see us at ASMS this year. Sneak peak at our new metabolomics product, Elements, for Metabolomics. Scaffold perSPECtives has new features, including label free quantitation and an interactive heatmap.
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  • Newsletter 10 - Spring 2014 : Volume 6, Issue 1
  • Come see us at ABRF, US HUPO and ASMS this year. Scaffold, Q+ and Q+S have been updated and released with many new features. Q+ and Q+S now support iTRAQ and TMT data from MaxQuant. Additionally, TMT 10-plex and 8-plex are supported as well as dimethyl quantitation from MaxQuant and Proteome Discoverer.
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  • Newsletter 9 - Fall 2013 : Volume 5, Issue 3
  • Come see us at HUPO in Japan, booth #42. Plus, we launched a new product, perSPECtives, that allows flexible analysis and organization of large-scale proteomics experiments, with robust, iterative filtering to find proteins of interest. Adaptive differential expression coloring to make changes pop.
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  • Newsletter 8 - Summer 2013 : Volume 5, Issue 2
  • Come see us at ASMS at booth #62. Plus, User's Group Meeting on Sunday, June 9th, 2013, 230pm. Our flagship product, Scaffold 4 is stable at 4.0.5. New FDR filtering, GO Term comparison by category, more robust statistics and compatibility with MaxQuant label-free quantitation.
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  • Newsletter 7 - Spring 2013 : Volume 5, Issue 1
  • Our flagship product, Scaffold 4 has been released! New FDR filtering, GO Term comparison by category, more robust statistics and compatibility with MaxQuant label-free quantitation.
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  • Newsletter 6 - Fall 2012 : Volume 4, Issue 2
  • How to queue structured directories for easily loading complex experiments that have multiple categories and biosamples; ASMS presentation describing non-parametric statistical methods used in Scaffold Q+ and Scaffold Q+S; User Group presentation about Scaffold PTM 2.0 features such as global motif analysis, quantification at modification sites and localization filtering; Proteome Software is distributing Mascot Distiller in the USA; Scaffold supports Spectrum Mill files; an early look at Scaffold 4.0; Scaffold Suite feature comparison table
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  • Newsletter 5 - Spring 2012 : Volume 4, Issue 1
  • SILAC quantitation with Scaffold Q+S; enhanced statistics in Scaffold Q+; computer memory settings for improved speed; what are Progenesis LC-MS and HDExaminer?
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  • Newsletter 4 - Fall 2011 : Volume 3, Issue 2
  • MassQC standalone; custom gene ontology annotations; Scaffold reads Proteome Discoverer MSF files; enhanced Scaffold Batch features; computer memory settings for improved speed; Scaffold PTM batch; we distribute Sierra Analytics HDExaminer
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  • Newsletter 3 - Winter 2011 : Volume 3, Issue 1
  • MassQC standalone; grouping algorithm explained; configuring protein annotation preferences; label-free quantitation with Progenesis LC-MS; Scaffold Batch
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  • Newsletter 2 - Winter 2010 : Volume 2, Issue 1
  • The what, why, how of MassQC! Learn about LC-MS quality control in the field of proteomics. System variability, instrument performance and more...
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  • Newsletter 1 - Winter 2009 : Volume 1, Issue 1
  • Create reverse FASTA databases; MassQC is coming; journal article on the importance of correct peptides and proteins in complex mixtures; Scaffold Q+ is launched; downloading GOA database; Scaffold Batch