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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.

InsPecT is a tool for interpreting peptide tandem mass spectra. Inspect searches spectra against a protein database. For each spectrum, Inspect reports the database peptide which best explains the spectrum, as well as a score indicating the confidence of this match.

Inspect was developed at the University of California, San Diego and the project homepage is http://peptide.ucsd.edu/. Inspect is free for educational, research, and non-profit purposes.

MS-Alignment algorithm for "blind" spectral search, with no bias toward anticipated modification types. This search has been applied to annotate heavily-modified proteins such as crystallins.

PepNovo uses a probabilistic network to model the peptide fragmentation events in a mass spectrometer. The de novo sequencing method is useful where the traditional database search cannot be used. For instance, to be able to offer the relevant candidate peptides for a database search, the target organism's genome must be sequenced and many organisms are still not sequenced.

PepNovo was developed at the University of California, San Diego and the project homepage is http://peptide.ucsd.edu/. PepNovo is free for educational, research, and non-profit purposes.

MS-Cluster is designed to rapidly cluster large MS/MS datasets. The program merges similar spectra (having similar m/z values - within a given tolerance), and creates a single consensus spectrum as a representative. The input formats accepted are: dta, mgf, mzXML. The output format is mgf. Checking this option will speed up the InsPecT/MS-Alignment search by pre-clustering the spectrum files.

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 arvhie.

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.

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 one Dalton shits, 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.

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.

Suggested values here are 1 and 2.

Residues must be a string of abbreviation letters for standard amino acid (i.e. ACDEFGHIKLMNOPQRSTUVWY). Fill in this field with an asterisk * if any residue will fit in your experiment.

Specify the minimum modification size (in Daltons) to consider. (default -200).

Specify the maximum modification size (in Daltons) to consider. Large values require more time to search (default 200).

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.

Specify the name of a FASTA-format protein database to search.

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).

Each real sequence in the database is shuffled to produce a decoy sequence. The presence of decoy sequences makes post-processing more reliable.

When job is done, you will get a notofication via the email address you specify here.

If the box is checked, the program uses the charge specified in the spectrum file (if charge=0, the program will try to guess the charge).

If the box is checked the program uses the exact precursor m/z as it appears in the spectrum file (no correction is done for ± Da errors).

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