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Introduction to Proteomics

The field of proteomics is complex and diverse in both process and application. To introduce some of the concepts of proteomics, we at Proteome Software have compiled a list of resources for the education of our community.

Introductory Essay on Proteomics

This essay answers questions like, What Are Proteins?; What Is A Proteome?; How Are Proteins Identified?; How Do Mass Spectrometers Work?; and many more useful foundations for understanding some of the basics. Those more familiar with the concepts can find some more advanced resources below.

For more specific information on how bioinformatics informs how our software operates, see our page on Bioinformatics.

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.


MS MS Data Analysis

Validating Sequence Assignments for Peptide Fragmentation Patterns: A Primer in MS/MS Sequence Identification
(Guest Publication from 2005)

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

Organizing MS/MS Proteomic Data for Publication with Scaffold
(Powerpoint presentation from the 2009 ABRF)

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

Using MS MS Total Ion Count (TIC) Quantification in Scaffold 3 Software - Comparison to Spectral Counting (2011)
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The Effect of Data Analysis Choices on the Number of Proteins Identified in MS MS Proteomics Experiments (2006)
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Tools for Proteomics

Ascore Explained
(Powerpoint presentation from 2010)

X! Tandem Explained
(Powerpoint presentation from 2005)

Use of Multiple Peptide Identification Programs to Increase Peptide and Protein Identifications in Human Whole Saliva (2006)
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Scaffold: A Program to Probabilistically Combine Results from Multiple MS MS Database Search Engines (2005)
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