You can contribute to <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 to easily run multiple search engines?<br><br>Try <a href="http://compomics.github.io/projects/searchgui.html">SearchGUI</a>!
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>Using 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 reviewed <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 and Comet do not support terminal modifications at specific amino acids.<br><br>SearchGUI searches allowing modification on all termini and PeptideShaker filters out unwanted peptides when loading the files. To turn off this feature uncheck <i>Exclude Unknown PTMs</i> in the <i>Import Filters</i>.
<i>Coverage 65% of estimated 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 your 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.
Share your results on <a href="http://www.proteomexchange.org/">ProteomeXchange</a> <i>via</i> the <a href="http://www.ebi.ac.uk/pride/">PRIDE</a> repository!<br><br><b>PeptideShaker</b> supports direct conversion to <a href="http://www.psidev.info/mzidentml">mzIdentML</a> via the <i>Export</i> menu.
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 solution: <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>.
<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).
PTM localization scores?<br><br><b>PeptideShaker</b> scores the localization of every PTM using the <a href="http://onlinelibrary.wiley.com/doi/10.1002/pmic.201200408/abstract">D-score</a> and a probabilistic score - either <a href="http://www.ncbi.nlm.nih.gov/pubmed/16964243">A-score</a> or <a href="http://pubs.acs.org/doi/abs/10.1021/pr200611n">PhosphoRS</a>. You can change these settings by editing the <i>Processing Preferences</i> when creating a new project.
Non-confident PTM localization?<br><br>Whenever a PTM is not confidently localized on a peptide it will appear with a white background and will not be displayed in the protein sequence.
Interested in PTM localization?<br><br>Try our protein level PTM export via <i>Identification Features</i> in the <i>Export</i> menu.
Interested in phosphorylation?<br><br>Try our phosphorylation export via <i>Identification Features</i> in the <i>Export</i> menu.
Using large databases?<br><br>When using large databases the import of your files will be slower and the results will contain more false positives. Be sure to calibrate the database to your need.
Need exports for algorithm training or spectral libraries?<br><br>Contact us at our <a href="http://groups.google.com/group/peptide-shaker">mailing list</a>!
PeptideShaker runs a lot faster on SSD discs!<br><br>Given that a lot of information is extracted from the mgf and FASTA files it is recommended to store these on an SSD disc!
Terminal modifications on degraded proteins?<br><br><b>PeptideShaker</b> excludes all protein terminal modifications which do not occur at the terminus of a protein sequence or on the second amino acid when the first is a methionine. If you need more flexible modification mapping use modifications at peptide termini.
Doubtful matches?<br><br><b>PeptideShaker</b> flags low confidence validation with a yellow warning icon. Clicking on the icon will provide you all details!
Using <b>PeptideShaker</b> without <b>SearchGUI</b>?<br><br>Don't forget to provide the identification parameters when creating a project!
Running out of disc space?<br><br>An index file is created for every protein database. You can select the folder where to store these indexes and clean it using the <i>Advanced</i> button of the database selection dialog.
When should I update my tool?<br><br>New versions are frequently released for a constant improvement of our tools. You will be notified if the tool can connect the internet. 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).
What is the best music to listen to when running PeptideShaker?<br><br>Click <a href="https://www.youtube.com/watch?v=Ilj-1sCr6y4">here</a> to enhance your shaking experience! &#9786;
Missing gene/chromosome information? Gene and Chromosome information is downloaded automatically from the <a href="ensembl.org/biomart">Ensembl biomarts</a>. Make sure that you are using a UniProt database, that your species is annotated in Ensembl, and that the tool has access to the internet.
How to operate PeptideShaker from other applications?<br><br>You can run PeptideShaker <i>via</i> <a href="http://compomics.github.io/peptide-shaker/wiki/peptideshakercli.html">command line</a>. The parameters can be provided in command line or as json files.
Working with labeled peptides?<br><br>Search a couple of files with variable modifications and then check the labeling efficiency in the peptide <i>Modification Efficiency</i> plot in the <i>QC Plots</i> tab!
<b>Fixed</b> or <b>Variable</b> modification?<br><br>Search a couple of files with all variable and then check the site modification rate in the peptide <i>Modification Efficiency</i> plot in the <i>QC Plots</i> tab!
Which modifications to search?<br><br>Try different combinations and evaluate the results in the <i>#Modification</i> plot in the <i>QC Plots</i> tab!
Working with enriched peptides?<br><br>Check the enrichment specificity in the peptide <i>Modification Specificity</i> plot in the <i>QC Plots</i> tab!
Questions on Proteomics?<br><br>Ask them at <a href="http://qa.proteomics-academy.org">qa.proteomics-academy.org</a>!
Looking for training?<br><br>Find courses on the <a href="http://proteomics-academy.org">Protomics Academy</a>!
Designed a bioinformatics workflow?<br><br>Write a tutorial on the <a href="http://wiki.proteomics-academy.org">Educational Wiki</a> of the <a href="http://proteomics-academy.org">Protomics Academy</a>!
Want to use SearchGUI and PeptideShaker in Galaxy? Try the <a href="https://github.com/Stortebecker/training-material/tree/master/Proteomics">Galaxy-P tutorials</a>!