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.

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.

Accepted formats: 32 bit uncompressed mzXML (preferred) and mgf.

Pick a single spectral library from the speclibs folder. If you do not have access email miw023@cs.ucsd.edu for access.

Minimum cosine score for consideration in a network.

Minimum peaks matching between two spectra to be in consideration for network.

Number of neighbors to retain in the network.

Minimum of spectra to be in a cluster for cluster be considered in network. Requires clustering to be turned on.

Maximum size of connected component to allow in network. Larger networks will be broken by increasing cosine threshold on that particular component and not globally.

Input text file organizing input files into groups.

Input text file organizing groups into attributes. These attributes are columns in the output.

Minimum cosine score for consideration in library search.

Minimum peaks matching between two spectra to be in consideration for library search.

For each spectrum the 25% least intense peaks are collected and the std-dev is calculated as well as the mean. A minimum peak intensity is calculated as mean + k * std-dev where k is user selectable. All peaks below this threshold are deleted.

All peaks below this raw intensity value are deleted.

All peaks +/- 17Da around precursor mass are deleted.

Apply all of these filters to library spectra as well before searching.

For each peak in spectrum to be kept, it must be at least 6th most intense peak in a window +/- 50Th around its m/z.

The quality of the library spectrum source in addition to the trust of the annotation.

Source of the ions.

Type of instrument to fragment and acquire the spectra.

Ionization mode, positive or negative.

Original source of the compound.

Principle Investigator of the new spectrum.

Data Collector of spectrum.

Specify the precursor ion tolerance, in Daltons. The value will be used only if Running Mode is set to 'custom'. Otherwise, default value for 'low' mode is 0.5 Da, for 'high' mode is 0.02 Da.

Specify the product ion tolerance, in Daltons. The value will be used only if Running Mode is set to 'custom'. Otherwise, default value for 'low' mode is 0.5 Da, for 'high' mode is 0.02 Da.