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Introduction to Bioinformatics in the Scaffold Software Suite

In many ways, Scaffold is a tool for analyzing statistics and presenting the data in a format that is easy to understand. However, the calculations can be complex. For an introduction into how the Scaffold Software Suite handles statistics, see Mark Turner's essay on the topic, "Question Assumptions". This essay addresses various topics such as, Filters for Peptides and Proteins; Scatter Plots and Combining Multiple Search Engines; and Protein Probabilities Derived from Peptides.

See our Proteomics page for resources pertaining to the field.

For a full list of our posters and presentations, as well as white papers, scientific journal article citations, and a wide range of other informative websites, check out our Resource Library.


Grouping Algorithm Explained: Understanding the Intricacies of Protein Grouping in Scaffold
(White paper from 2011)

High Mass Accuracy Scoring
(White paper from 2010)

Normalizing Spectral Counts in Scaffold
(White paper from 2010)

Reporting Protein Identifications from MS/MS Results
(Powerpoint presentation from the ASMS 2009)

Interpreting MS/MS Proteomics Results
(Powerpoint presentation from the NPC Progress Meeting, 2006)

X! Tandem Explained
(Powerpoint presentation from 2005)

PeptideProphet Dissected
(PDF presentation from the Proteomics Interest Group 2005)

Testing for Differences Between Complex Samples in Proteomics Datasets (2009)

Improving Sensitivity by Combining MS MS Results (2007)

Identifying Peptides the Way Experts Do: A Scientist-Driven Scoring System for Improving MS MS Peptide Identification Confidence (2006)

Improving Computer Interpretation of Linear Ion Trap Data Using Scaffold (2006)

The Effect of Data Analysis Choices on the Number of Proteins Identified in MS MS Proteomics Experiments (2006)

Scaffold: A Program to Probabilistically Combine Results from Multiple MS MS Database Search Engines (2005)

Scaffold Q+ and Q+S

Advancing Statistical Analysis of Multiplexed MS/MS Quantitative Data with Scaffold Q+
(Powerpoint presentation from the ASMS 2012)

Kernel Density Function for Protein Abundance
(White paper from 2012)

The Randomized Permutation Test
(White paper from 2012)

Normalization in Q+
(White paper from 2012; adapted from the ASMS 2012 Powerpoint presentation)

Treatment of Missing Values in Q+
(White paper from 2012)

Quantification Setup in Scaffold Q+ 3.4.0
(White paper from 2011)

Quantitation Across Multiple iTRAQ Samples Using Scaffold Q+ (2009)

Scaffold PTM

Ascore Probability Description
(White paper from 2011)

Ascore Explained
(Powerpoint presentation from 2010)

Probabilistically Assigning Sites of Protein Modification with Scaffold PTM (2011)