Copyright © 2013.
Last modified: 2013-08-23.
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
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
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
Attach a custom license file describing the terms and limitations under
which this dataset will be released.
Files describing the methods and protocols used to generate this dataset.