proteomics data analysis using galaxy-p august 11th 2016 ......center for mass spectrometry and...

Center for Mass Spectrometry and Proteomics | Phone | (612)625-2280 | (612)625-2279

© 2015 Regents of the University of Minnesota. All rights reserved.

Proteomics Data Analysis using Galaxy-P

Center for Mass Spectrometry and Proteomics

August 11th 2016

Pratik Jagtap

http://www.cbs.umn.edu/msp

©2016 Regents of the University of Minnesota, All rights reserved.





Documentation: http://z.umn.edu/augworkshopgalaxyp


http://z.umn.edu/augworkshopgalaxyp





GALAXY PLATFORM

Benefits of Galaxy

• A web-based bioinformatics data analysis platform.

• Software accessibility and usability.

• Share-ability of tools, workflows and histories.

• Reproducibility and ability to test and compare results after using multiple

parameters.

• Software tools can be used in a sequential manner to generate analytical workflows

that can be reused, shared and creatively modified for multiple studies.

Goecks J et al Genome Biol. 2010;11(8):R86.




TOOLS & WORKFLOWS • Software tools can be used in a sequential manner to generate analytical

workflows that can be reused, shared and creatively modified for multiple studies.

For example, Protein Database Downloader

downloads UniProt protein FASTA

databases of various organisms.




Eng et al 2011 Mol Cell Proteomics. 10(11): R111.009522.

PROTEOMICS WORKFLOW




WORFLOW 1

INPUTS : PEAKLISTS and SEARCH db




Tools used in the workflow




Galaxy-P: https://galaxyp.msi.umn.edu/


https://galaxyp.msi.umn.edu/

https://galaxyp.msi.umn.edu/



INPUTS : Mass spectral data and search database.

The dataset will be searched against FASTA

database with human proteins, contaminant

proteins, spiked in proteins and a subset of 3-

frame translated cDNA database from

EnSEMBL.

INPUTS: a) MGF formatter MGF files.

(dataset collection)

b) ABRF-Spike4: FASTA sequences of 4

spiked in proteins.

c) FASTA File from EnSEMBL Searches:

Subset of 3-frame translated cDNA database

from EnSEMBL (our template for identifying

novel proteoforms).

d) Human UniProt FASTA file + contaminant

proteins.

HeLa cell lysate

4 proteins spiked in

(10 fmols each)

Digested O/N with trypsin

Liquid chromatography fractionation

(10 fractions)

Thermofinnigan Orbitrap Velos (Orbi MS,

MS/MS HCD)

RAW Files

mzml files

msconvert

MGF files ©2016 Regents of the University of Minnesota, All rights reserved.



RAW DATA CONVERSION TOOL

.RAW

msconvert ProteoWizard

mzML

http://z.umn.edu/msconvert

MGF Formatter

MGF

http://z.umn.edu/mgfformatter


http://z.umn.edu/msconvert





Log in using your MSI login and password.

Click on http://z.umn.edu/history3

SEARCHING MS/MS SPECTRA A DATABASE

1

2


http://z.umn.edu/history3

http://z.umn.edu/history3



Eng et al 2011 Mol Cell Proteomics. 10(11): R111.009522.

PROTEOMICS WORKFLOW




INPUTS : Mass spectral data and search database.

The dataset will be searched against FASTA

database with human proteins, contaminant

proteins, spiked in proteins and a subset of 3-

frame translated cDNA database from

EnSEMBL.

INPUTS: a) MGF formatter MGF files.

(dataset collection)

b) ABRF-Spike4: FASTA sequences of 4

spiked in proteins.

c) FASTA File from EnSEMBL Searches:

Subset of 3-frame translated cDNA database

from EnSEMBL (our template for identifying

novel proteoforms).

d) Human UniProt FASTA file + contaminant

proteins.

HeLa cell lysate

4 proteins spiked in

(10 fmols each)

Digested O/N with trypsin

Liquid chromatography fractionation

(10 fractions)

Thermofinnigan Orbitrap Velos (Orbi MS,

MS/MS HCD)

RAW Files

mzml files

msconvert




Select History 1

Import history

Start using this history

Select Workflow 1

Import workflow

Start using this workflow

Run Workflow 1

INPUT

WORKFLOW




A face in the crowd: recognizing

peptides through

database search.

Eng et al 2011 Mol Cell

Proteomics. 10(11)

PROTEOMICS WORKFLOW




Visualizing parameters for SearchGUI analysis




SEARCHGUI

Vaudel M. et al Proteomics (2011) 11(5)

https://code.google.com/p/searchgui/







PEPTIDESHAKER

Vaudel et al Nature Biotechnology, 33, (2015)

http://galaxyproteomics.github.io/peptideshaker/




4.3 Peptide Shaker in GalaxyP




PEPTIDESHAKER: OUTPUTS




QUESTIONS?

Follow us on twitter.com/usegalaxyp

Visit

http://galaxyp.msi.umn.edu

or


http://z.umn.edu/galaxypinterest




proteomics data analysis using galaxy-p august 11th 2016 ......center for mass spectrometry and...

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