Agilent Technologies Spectrum Mill MS G2721AA Quick Start Manual Download Page 20

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Agilent Technologies

Agilent Technologies, Inc. 2007

Printed in USA
Fifth edition, June 2007

*G2721-90028*

G2721-90028

www.agilent.com

In this Book

The

Quick Start Guide

presents first steps to use
the Spectrum Mill MS
Proteomics Workbench.

Summary of Contents for Spectrum Mill MS G2721AA

Page 1: ...e includes bioinformatics tools for Spectral preprocessing for MS MS and MS only data including spectral quality filtering and precursor charge state assignment for MS MS spectra Protein database sear...

Page 2: ...rch peptides that have a charge up to 7 New Maximum ambiguous precursor charge which allows you to choose the maximum charge state that you want MS MS Search to consider when the Data Extractor could...

Page 3: ...Deamidated N and Deamidated Q as variable modifications The software displays the first by default system administrators can add the second by copying a definition from smconfig misc xml to smconfig...

Page 4: ...batches and to apply them to the iTRAQ calculations for specific data sets Expanded capabilities for Peptide Selector Updated instrument selection lists The default Spectrum Mill font size is now smal...

Page 5: ...overview of the optional Generic Data Extractor for peak list files QSTAR Data Extractor Quick Start Guide Get a quick overview of the optional Applied Biosystems MDS Sciex QSTAR Data Extractor System...

Page 6: ...7 0 1 Open Internet Explorer 2 Select Help About Internet Explorer Java Check that Internet Explorer on the client is configured for Sun JRE 1 5 x also called J2SE 5 0 or Java SE 6 You can get a comp...

Page 7: ...d instructions to enable cookies search Internet Explorer help for cookies 4 If the drop down menus in the Spectrum Mill workbench appear empty you may need to add the Spectrum Mill server as a truste...

Page 8: ...ation Guide Software Status Bulletin and software patches A list of known problems for the Spectrum Mill workbench along with possible solutions is found on the Agilent Web site 1 Go to http www agile...

Page 9: ...ch Search MS MS spectra against databases 1 Spectrum Matcher Match MS MS spectra against other MS MS spectra 1 de novo Sequencing Use Sherenga de novo sequencing to interpret MS MS spectra 1 3 PMF Sea...

Page 10: ...hat meet certain criteria e g likely to produce high quality MS MS spectra 8 Multiple Sequence Aligner Align amino acid sequences of proteins from a database and highlight the amino acids that differ...

Page 11: ...nt results or export to Excel LIMS HTML or PowerPoint Search unmatched spectra against a larger database and validate results Start here Collect and transfer data to Spectrum Mill server Search in var...

Page 12: ...llowing common modifications into a single search oxidized methionine methionine sulfoxide and pyroglutamic acid N terminal b If you suspect phosphorylation combine the following modifications into a...

Page 13: ...want to process the data further Search another database and review results PMF Search page and PMF Summary page Basic workflow Optional workflow Key No Yes Prepare a final results summary PMF Summary...

Page 14: ...irectory Proteins then redundant hits Protein Protein Comparison Redundant Same as immediately above with additional detail on isoforms of proteins Proteins then peptides Protein Summary Details View...

Page 15: ...a data directory for this and subsequent forms Mark the Make Default check box to retain this directory for future web browser sessions Choose Selects peptide modifications If you wish to view details...

Page 16: ...hit Guidelines for validating ion trap results based on MS MS Search scores Guidelines for validating Agilent Q TOF results based on MS MS Search scores Because the mass accuracy is better than with...

Page 17: ...Spectrum Mill Workbench Quick Start Guide 17...

Page 18: ...18 Spectrum Mill Workbench Quick Start Guide...

Page 19: ...Spectrum Mill Workbench Quick Start Guide 19...

Page 20: ...ies Agilent Technologies Inc 2007 Printed in USA Fifth edition June 2007 G2721 90028 G2721 90028 www agilent com In this Book The Quick Start Guide presents first steps to use the Spectrum Mill MS Pro...