Workflow Selection

Workflow Submission
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Copyright © 2014. Last modified: 2014-04-17. Version 1.2.6.

You can perform a restrictive search with InsPecT, where a collection of pre-specified modifications are permitted, or an unrestrictive (or "blind") search, using the MS-Alignment algorithm, to discover unanticipated modifications and point mutations.

PepNovo serves as a high throughput de novo peptide sequencing tool for tandem mass spectrometry data.
Search protocols are saved workflow parameter sets. You can save a new protocol by filling out this form, and then selecting "Save as Protocol" below, which will record the contents of the form and save it to your list of protocols. Then, selecting a saved protocol from the list to the right will automatically populate this form with all of the values stored in that protocol. All parameters except input files and task description are included when a protocol is saved.
When your task is done, you will get a notification via the email address you specify here.
Accepted formats: mzXML (preferred), dta, pkl, and mgf. Archived files (zip, gz, bz2, tar.gz, tar.bz2) are supported too; you can put multiple spectrum files of an experiment in a single archive.
The type of mass spectrometer used to generate the experimental spectra.
ESI-ION-TRAP (default) - InsPecT attempts to correct the parent mass.
QTOF - InsPecT uses a fragmentation model trained on QTOF data. (QTOF data typically features a stronger y ladder and weaker b ladder than other spectra).
High accuracy LTQ - an FT-LTQ or an orbitrap.
The fragmentation method used.
The chemical modification used to treat the cysteine residues in the peptide (typically a +57 Carbamidomethylation is used).
Specifies the name of a protease. "Trypsin", "None", and "Chymotrypsin" are the available values. If tryptic digest is specified, then matches with non-tryptic termini are penalized.
Number of allowed C13.
Number of allowed non-enzymatic termini.
Specify the parent mass tolerance, in Daltons. Default value is 2 Da. Note that secondary ions are often selected for fragmentation, so parent mass errors near 1.0 Da or -1.0 Da are not uncommon in typical datasets, even on FT machines; therefore, the program examines ± Da shifts even if a low precursor tolerance is selected. If you are sure there are no Dalton shifts, you should check the box "use spectrum precursor m/z".
Specify how far b and y peaks can be shifted from their expected masses. Default is 0.5.
Suggested values here are 1 and 2.
Select a database to search. As databases are updated regularly, the timestamp of the last modification is specified in paranthesis. For faster searches InsPecT uses internally the (.trie) file format.
Searches a small database of common protein contaminants of proteomics searches: trypsin (TRYP_PIG, TRYP_BOVIN) and keratin (K22E_HUMAN, K22O_HUMAN, K2C1_HUMAN, K2C3_HUMAN, K2C7_HUMAN, K1C1_HUMAN).
Specify the name of a FASTA-format protein database to search.
Spectrum-Level False Discovery Rate
False Positive Rate
See the MS-GF documentation for more information.
Attach a custom license file describing the terms and limitations under which this dataset will be released.
Submit this dataset under the Creative Commons CC0 1.0 Universal license. For more information on this license, visit the Creative Commons site:
Files describing the methods and protocols used to generate this dataset.