There
is a predefined set of submission profiles available at top of
the
Submission page. You can perform a preliminary search selecting the
Profile corresponding (or nearest from)
your
workflow: the parameters associated to this profile will be loaded into
the
Submission page. Depending on the results accuracy, you can resubmit
the job modifying the parameters and saving your own submission profile.
Yes, you can avoid enzymatic cleavage by selecting "DoNotCleave" in the Enzyme drop down Menu on the Submission Page. The protein will remain entire as such selection means "Does not cleave at all".
If you are looking for non-tryptic cleavage, you can select "half-cleaved" in the "cleav. mode" drop down menu.
For more detailed information about enzymatic cleavages, please refer to the User Manual.
Fully
functional unspecific
cleavage option is solely available in a local Phenyx installation or
in the secured Phenyx OnLine Server. The public server only accepts
fully specific and semi-specific cleavages. To select semi-specific
cleavage in the submission form, choose "half-cleaved" in the
Cleavage Mode drop down menu: enzymatic digestion
will occur specific to the enzyme rules at one peptide
terminus (either C- or N-terminus) and nonspecific at the
other.
Compared to a fully specific or a semi-specific cleavage, the fully
unspecific cleavage option requires a much longer calculation time.
Limitation is set on the public server to allow a better share of
CPU time to a maximum of users.
If your protein is in a sequence databank, such as Uniprot Swiss-Prot, select the desired database(s), then select "NO_TAXONOMY" as taxonomy restriction and define the AC of your entry (eg. P23456) in the "AC List" field.
Use compressed files such as .zip or tar.gz (only peaklist files must be packaged). For more information, see http://en.wikipedia.org/wiki/ZIP_(file_format) and http://en.wikipedia.org/wiki/Tar_(file_format)
Processed peaklists formats from major MS hardware and software providers are accepted; accepted peaklists file formats include dta (Sequest format), pkl (Micromass format), mgf (Mascot generic format), bdtx (Bruker XML format), mzData (HUPO Proteomics Standards Initiative international XML format), mzXML (Institute for Systems Biology XML format). We have decided not to include any peak detection algorithm to process binary or ascii complete traces at the moment. We believe that it is an evolving specificity of the MS instrument providers to provide this information. The instrument providers we are discussing with agree with this principle. We do prefer to adapt Phenyx scoring schemes and thresholds to the level of quality of these algorithms' outputs (and to other internally developed peak picking algorithms) than to propose and impose our own system. This allows end-users to develop a data analysis workflow (possibly including a LIMS system) that always uses the same data for different identification tools, or to send the data from different instrument to only one protein identification tool.
To convert wiff files into dtas and then submit them to Phenyx, we recommend the use of wiff2dta, a software freely available at http://sourceforge.net/projects/protms/
To convert raw data to mzXML format (Phenyx accepted submission format), please see http://sashimi.sourceforge.net/software_glossolalia.html
If your specific instrument is not in the list, you can select an instrument type and algorithm that correspond to an instrument with characteristics as similar as possible to your instrument and workflow type (if applicable). You can also select the default algorithm for the instrument type of your choice. If you have purchased a local Phenyx license, please contact us and we'll learn a new scoring specific to your instrument(s) and workflow.
To copy/paste your MS/MS data, you can use Microsoft Notepad and save your file as a .txt file. When you submit your file to Phenyx, simply make sure you select the corresponding file format.
Those files will be sent as one (merged) and you'll get a single result file.
You
can perform
automated submissions of MS/MS spectra to Phenyx with the Phenyx
Daemon, and even other automated actions (e.g. data filtering,
format conversion...). Please visit
our "Feature and Benefits" section at http://www.phenyx-ms.com/about/features.html#section6
to know more
about the Phenyx Daemon capabilities. Do not hesitate to contact us at
Phenyx@genebio.com to request an evaluation copy and for pricing
information.
.
Phenyx gives you the possibility to create your own enzymatic rules and amino acid modifications. The procedure is described in the Phenyx User manual available from the "Documentation" link on the Phenyx Desktop top menu or here.
In order to implement changes in Phenyx, you must Log Out and then Log In again.
In the Phenyx Desktop, select your job number, then select "Kill" in the "Actions on Selected" drop down menu. The job will remain in the Desktop table, but its status will change (red flag) and the "Comment" column will show the following message: "killed" (or sometimes "Sigtap.INT").
In the Phenyx Desktop, select your job number, then select "Delete" in the "Actions on Selected" drop down menu. Your job will then disappear from the Desktop.
In the Desktop, select your job number, then click on "Parameters" in the left hand side menu. You also can access this page via the "Parameters" link in the Protein Overview page. To compare the search parameters of several jobs, simply check the boxes corresponding to the jobs you wish to select, then go to the "Actions on Selected" drop down menu and click on "Parameters".
In the Desktop, select your job number, then click on "Resubmit" in the left hand side menu. The original data will automatically be uploaded unless you deselect the corresponding box. You can also add new data with a different format.
You can save a set of parameters as a new Profile by using the "Save as Profile" button in the Submission page. Then use this Profile to submit new jobs.
If you want to perform identification on sequences not present in the databases already available in the Submission form, it is possible to easily create your own private database via a simple interface. This feature is available in the local version of Phenyx or in the Phenyx OnLine server.
Yes. As for MS2 data,
information about the precursor of MS2 has to be provided together with
the MS3 spectrum. Are you analysing
fragmentation of
products from neutral losses, for instance in the analyses of
phosphopeptides? MS3 activated on peptides that have lost the H3PO4
(neutral loss) can be analysed as if they were peptide with a simple
PTM defined as -H2O on S or T. For fragmentation of other
ion types, the
definition of the modification should be attributed accordingly, and
the "precursor" fragment charge should also be considered in the
calculation.
In the Phenyx Desktop, select your job number, then select "Kill" in the "Actions on Selected" drop down menu. The job will remain in the Desktop table, but its status will change (red flag) and the "Comment" column will show the following message: "killed" (or sometimes "Sigtap.INT").
In the Phenyx Desktop, select your job number, then select "Delete" in the "Actions on Selected" drop down menu. Your job will then disappear from the Desktop.
Phenyx results can be exported and archived in various format. From the Phenyx desktop window, select a job by clicking on its job ID, then click on the Export Text link on the left-hand job menu to access a list of specific exports. Note the 'MCP Excel worksheet global export' that supports international standards.
Go to the Management Console > Jobs Management > export/browse files: click on the Help button to access the Wiki information page about exports.
Use the Export options at the bottom of the table.
Go to the Management Console > Jobs Management > import: select the corresponding option and paste the results data either browsing to locate the file or copying/pasting the complete URL. Caution, the URL must be accessible from the Phenyx server.
Click on the Help button to access more information.
Once imported, the jobs are available on the Desktop. Select the jobs and choose Compare from the Actions on Selected drop-down menu to access the Results Comparison page.
Yes. You can verify the peptide match accuracy through the Peptide Match Details View (graphical display with information on signal intensities and errors on m/z). You can then manually change the validation status of your peptide match in the Compound View Page, using the Manual Validation features.
Experimental elution times for mgf files are taken by parsing the TITLE=line of the precursor. A regular expression to parse your MSMS software output does not exist in the current InSilicoSpectro perl module release. Please send us your mgf peaklist and we will try to find a way to parse and report this information.
current InSilicoSpectro perl module release. Please send us your mgf peaklist and we will try to find a way to parse and report this information.
Yes. Phenyx integrates the true probabilistic and flexible scoring system OLAV which has been published and described in publicly available literature (see "Further readings" in our documentation page on http://www.phenyx-ms.com/).
During the processing of the peptide z-score calculation, one step estimates the probability of a random match for each spectrum. A population of randomly sampled peptides is generated for each spectrum, that constitutes a random database, and is matched against the experimental spectrum. This set of peptides is different for each calculation. Therefore the probability of a random match can slightly vary from one identification result to the other. Usually this does not exceed 10% of the z-score value.
For some of these jobs, the result variability may cause peptides (and therefore proteins) with score values close to the thresholds ("low scores") to jump below the acceptance criteria provided in the submission parameters (see explanation provided in "Why do the scores slightly vary when I resubmit a job several times?"). When lowering the acceptance criteria threshold values, you may retrieve an increasing number of matches including an increasing number of false positive matches. Thus, this population of false positive peptide will consequently vary when resubmitting a job.
Phenyx gets information on Database annotations. It looks at protein forms and not only at main protein entries in a sequence database. As databases like Swiss-Prot and TrEMBL contain annotations of mature forms, splicing variants, mutations or PTMs, Phenyx looks at these annotations and generates the various forms of the protein entries. For more detailed information, please refer to the User Manual.
If occuring on the Phenyx public version, please send us