output
html_document

launch app with shiny::runApp(launch.browser = TRUE)

The Pepliner app is for viewing peptide or protein elution profiles

• In a fractionation-MS experiment, a protein sample is separated across a gradient into multiple fractions.
• Proteins are identified from each fraction independently.
• It's often necessary to visualized where a protein is detected across fractions.
• Pepliner is a suite of R functions and a shiny app for viewing patterns of detection of peptides or proteins across multiple fractions.
• The main functions of this shiny are to:

1. Interactively select a series of proteins to plot (protein-level visualization)

2. Interactively plot peptides from a single protein (peptide-level visualization)

• Explore the app's features with the example data set pre-loaded by clicking on the tabs above.
• Upload your data in the "Input Data" tab.

Features

Visualize your data:

• Visualize elutions of peptides from single proteins
• Visualize elutions of multiple proteins across fractions

Data Format

• Must be a .CSV comma-separated-value file (you may export from Excel).
• File must have a header row.
• Depending on whether uploading protein-level or peptide-level data format as follows:

Protein data

• Must be a .CSV comma-separated-value file (you may export from Excel).
• Upload data either in wide or tidy format
• Tutorial on wide vs. tidy data

Wide format

• Must contain a column called ID, with remaining columns rightward representing individual fractions
• Each row is a proteins's detection across fractions

ID	Fraction1	Fraction2	Fraction3
ProteinA	0	1	3
ProteinB	5	25	10

Tidy format

• Must contain columns ID, ProteinCount, FractionID (in any order)
• Each row is a protein's detection in a single fraction

ID	FractionID	ProteinCount
ProteinA	Fraction1	0
ProteinA	Fraction2	1
ProteinA	Fraction3	3
ProteinB	Fraction1	5
ProteinB	Fraction2	25
ProteinB	Fraction3	10

Peptide data

• Must be a .CSV comma-separated-value file (you may export from Excel).

Wide format

• Must contain a columns called Peptide and ID, with remaining rightward columns representing individual fractions
• Each row is a peptide's detection across fractions.

Peptide	ID	Fraction1	Fraction2	Fraction3
AAGTEPR	ProteinA	0	1	1
CNMETLLK	ProteinA	0	0	2
IPRELVK	ProteinB	2	12	2
MITFPELLR	ProteinB	3	13	8

Tidy format

• Must contain columns Peptide, ID, PeptideCount, FractionID (in any order)
• Each row is a peptide's detection in a single fraction

Peptide	ID	FractionID	ProteinCount
AAGTEPR	ProteinA	Fraction2	1
AAGTEPR	ProteinA	Fraction3	1
CNMETLLK	ProteinA	Fraction3	2
IPRELVK	ProteinB	Fraction1	2
IPRELVK	ProteinB	Fraction2	12
IPRELVK	ProteinB	Fraction3	2
MITFPELLR	ProteinB	Fraction3	3
MITFPELLR	ProteinB	Fraction3	13
MITFPELLR	ProteinB	Fraction3	8

TIP: Save Data for Future Upload

After uploading your data to the pepliner app, click red button

to download an .RData file to upload your data to the pepline app with one click.

Next time use the "Input Data" tab --> "Pepliner RData file" option.

More Help and Info

Additional help information and more detailed instructions are provided under the "Instructions" tab.

App Info

Provenance

The source code for pepliner is available on Github.

A paper describing use of peptide elutions to identify proteoforms will be posted on BioRxiv.

Pepliner was modified from the START app developed by Jessica Minnier, Jiri Sklenar, Anthony Paul Barnes, and Jonathan Nelson of Oregon Health & Science University, Knight Cardiovascular Institute and School of Public Health.

Nelson, JW, Sklenar J, Barnes AP, Minnier J. (2016) "The START App: A Web-Based RNAseq Analysis and Visualization Resource." Bioinformatics. doi: 10.1093/bioinformatics/btw624.

The original source code of START is available on Github.