You can contribute to <i>SearchGUI</i> and <i>PeptideShaker</i>!<br><br>Use our <a href="http://groups.google.com/group/peptide-shaker">mailing list</a> to explain your special needs and exchange new ideas!
Post-Translational Modifications (PTMs) are color coded in <b>PeptideShaker</b>.<br><br>You can change the colors via <i>Search Parameters</i> on the <i>Edit</i> menu.<br><br>You can also verify the location of the PTMs in the <i>Modifications</i> tab!
Not getting the result you expected?<br><br>When creating a new project, be sure that the <i>Search Parameters</i> and <i>Import Filters</i> are correct!
How did you generate your mgf file?<br><br>Processing of the raw data can have dramatic impact on the final result.<br><br>More information in our <a href="http://compomics.com/bioinformatics-for-proteomics/">free tutorials</a>!
Need more help?<br><br>Look for the question marks.<br><br>We will also be happy to answer your questions on our <a href="http://groups.google.com/group/peptide-shaker">mailing list</a>.
Which database are you using?<br><br>Large databases increases the amount of false positive identifications.<br><br>Use only the species expected in the sample.<br><br>We recommend the use of <a href="http://uniprot.org">UniProt</a> databases.
<b>PeptideShaker</b> not finding your protein?<br><br>Verify that you are using the correct database and that no error occurred during the import of the FASTA file! <br><br><a href="http://compomics.github.io/searchgui/wiki/databasehelp.html">More help on databases</a>.
Did you expect more peptides/proteins?<br><br>Verify the search engine performance(s) in the <i>Spectrum IDs</i> tab. Adjust the validation settings in the <i>Validation</i> tab.<br><br><i>If comparing results with other packages, remember to use the same search, import and validation settings!</i>
Using Mascot?<br><br>Make sure that the database used is identical to the one provided to <b>PeptideShaker</b>.<br><br>And that the Mascot <i>decoy</i> option is <b><u>not</u></b> selected!
Did you check the QC plots?<br><br>Quality Control plots are available in the <i>QC Plots</i> tab.<br><br>That way you can verify that everything went OK during the identification process.
Need another QC metric/plot?<br><br>Propose it on our <a href="http://groups.google.com/group/peptide-shaker">mailing list</a>!
Too many/too few peak annotations?<br><br>Change the minimum peak intensity threshold by scrolling the mouse wheel. Or change the m/z accuracy by holding the control key while scrolling.<br><br>Controllers are available in the <i>View</i> menu under <i>Spectrum Sliders</i>.
Many unidentified spectra?<br><br>Export the unidentified spectra via <i>Follow Up Analysis</i> on the <i>Export</i> menu.
Create inclusion lists?<br><br>Inclusion lists can be automatically generated using the <i>Follow Up Analysis</i> dialog accessible from the <i>Export</i> menu.<br><br>If you have any questions don't hesitate to contact us using our <a href="http://groups.google.com/group/peptide-shaker">mailing list</a>.
Share <b>PeptideShaker</b> projects?<br><br>Export the project and related files as a zip file in the <i>Export</i> menu.<br><br>To open on another computer simply unzip the file and open the cps file in <b>PeptideShaker</b>!
Export results to Excel?<br><br>Export the entire project or specific identification features via <i>Identification Features</i> in the <i>Export</i> menu.<br><br>The files can then be directly opened in Excel!
Never run different instances of <b>PeptideShaker</b> from the same .jar file!
Investigate a specific Protein/Peptide/PSM?<br><br>See how to customize star/hide filters via <i>Filters</i> in the <i>Edit</i> menu.
Looking for a specific protein or peptide?<br><br>Use the <i>Find</i> box in the upper right corner!
To get the highest number of reliable hits, <b>PeptideShaker</b> separates PSMs according to search engine charge and peptides according to modification status. See the <i>Validation</i> tab.<br><br>Note that separation will only be conducted when statistical significance is ensured!
X!Tandem, MyriMatch and Comet do not support terminal modifications at specific amino acids.<br><br>Use a search allowing modified termini or amino acids and use <i>Exclude Unknown PTMs</i> in the <i>Import Filters</i> when loading the files.
<i>Coverage 65% of max 50%</i>?<br><br>The estimation of the maximum coverage does not account for missed cleavages or semi-tryptic peptides!
How much memory is allocated to <b>PeptideShaker</b>?<br><br>For fast processing allocate as much memory as possible to <b>PeptideShaker</b>.<br><br>This setting can be optimized in <i>Java Option</i> available in the <i>Edit</i> menu.
Find our tools useful?<br><br>Then please cite them in your papers!<br><br><b>SearchGUI</b>: <a href="http://www.ncbi.nlm.nih.gov/pubmed/21337703">Vaudel <i>et al.</i>: Proteomics 2011;11(5):996-9</a>.<br><br><b>PeptideShaker</b>: <a href="http://www.nature.com/nbt/journal/v33/n1/full/nbt.3109.html">Vaudel <i>et al.</i>: Nature Biotechnol. 2015 Jan;33(1):22-24</a>.
Need high quality graphics for you manuscript?<br><br>All plots in <b>PeptideShaker</b> can be exported in either high resolution or as vector graphics.<br><br>See the contextual menus in the upper right corners of each panel.
Submit your results to PRIDE!<br><br><b>PeptideShaker</b> supports direct conversion to <a href="http://www.psidev.info/mzidentml">mzIdentML</a> via the <i>Export</i> menu in PeptideShaker.
Label free quantification?<br><br><b>PeptideShaker</b> supports <a href="http://www.nonlinear.com/products/progenesis/lc-ms/overview/">Progenesis LC-MS</a> via the <i>Follow Up Analysis</i> option in the <i>Export</i> menu.
Troubles identifying your proteomics data?<br><br>Check our <a href="http://compomics.com/bioinformatics-for-proteomics/">free tutorials</a>!
Tried <i>de novo</i> sequencing?<br><br>Check out our user friendly <i>de novo</i> sequencing option: <a href="http://compomics.github.io/projects/denovogui.html">DeNovoGUI</a>!
Surprisingly large files?<br><br>Be sure that the data is in centroided mode and not in profile mode!<br><br>More information on peak-picking available in our <a href="http://compomics.com/bioinformatics-for-proteomics/identification/">free tutorials</a>.
Database import is slow?<br><br>The first time you work with a database <b>PeptideShaker</b> needs to index all the possible peptides.<br><br>This task is time consuming, but will be done only once for each database.
<b>Galaxy</b> + <b>PeptideShaker</b>?<br><br>Did you know it was possible to use <a href="https://usegalaxyp.readthedocs.org/en/latest/sections/peptideshaker.html">PeptideShaker in Galaxy</a>?
Unexpected mass deviations?<br><br>It is possible to export recalibrated spectra via <i>Follow Up Analysis</i> in the <i>Export</i> menu.
Need a graphical overview?<br><br>It is possible to export the protein identification data to <a href="http://cytoscape.org/">Cytoscape</a>, <a href="https://gephi.org/">Gephi</a> or <a href="http://www.neo4j.org/">Neo4j</a> via <i>Follow Up Analysis</i> in the <i>Export</i> menu.
Special requests for the design of the spectrum panel?<br><br>You can tailor-make the design via <i>Spectrum Annotation</i> in the <i>Edit</i> menu.
Special requests for the design of the spectrum?<br><br>You can change peak colors in the <i>Settings</i> menu under every spectrum.
Want to create your own report?<br><br>Try our <i>Custom Reports</i> via <i>Identification Features</i> in the <i>Export</i> menu.
Tired of writing <i>Materials and Methods</i>?<br><br>Check out our <i>Methods Section</i> export available in the <i>Export</i> menu.
Need a report for your collaborators?<br><br> Try our <i>Certificate of Analysis</i> available in the <i>Custom Reports</i> via <i>Identification Features</i> in the <i>Export</i> menu.
Reviewing a publication?<br><br>You can easily inspect <a href="http://www.proteomexchange.org/">ProteomeXchange</a> data in the <a href="http://www.ebi.ac.uk/pride/">PRIDE</a> repository using <a href="https://github.com/PRIDE-Toolsuite/pride-inspector">PRIDE Inspector</a>!
Found an interesting paper?<br><br>You can reprocess <a href="http://www.proteomexchange.org/">ProteomeXchange</a> data in the <a href="http://www.ebi.ac.uk/pride/">PRIDE</a> repository with just a few clicks using the <i>PRIDE Reshake</i> option in the Welcome Dialog!
Want to search published data for new modifications?<br><br>You can reprocess data in <a href="http://www.ebi.ac.uk/pride/">PRIDE</a> with just a few clicks using the <i>Reshake</i> option in the Welcome Dialog!
Teaching bioinformatics?<br><br>Check out our <a href="http://compomics.com/bioinformatics-for-proteomics/">free tutorials</a>!
Want to learn more?<br><br>Check out our <a href="http://compomics.com/bioinformatics-for-proteomics/">free tutorials</a>!
X's in your database?<br><br>X's in protein sequences make it difficult for <b>PeptideShaker</b> to interpret your results. Peptides with more than 75% X's will be ignored.
Unexpected peptide-protein mapping?<br><br><b>PeptideShaker</b> remaps every peptide to your sequence database. The peptide to protein mapping can be different - and more comprehensive - than the search engines.
Cannot find your peptide in the protein sequence using a text editor?<br><br><b>PeptideShaker</b> accounts for indistinguishable amino acids (like I and L) or amino acid groups (like B, J Z or X).
When should I update my tool?<br><br>New versions are regularly released for a constant improvement of our tools. You will be notified if the tool can connect the internet and it is advised to always keep your tools up to date.
How do results compare between versions?<br><br>Results cannot be compared between major releases (big number change) but between minor releases (small number change).