Help

This page describes each item in the user interface of Preview. To learn more, visit the About, Tutorial, and FAQ pages.  Also note the helpful information in the form of tool tips: simply hover the mouse cursor over the text on the application’s user interface to bring up these tool tips.

Input Files

These are the two required fields.

Select MS/MS data file

Input spectra in .mzML, mzXML, Thermo Raw, or mgf format. See Examples_to_test_with folder in Preview program folder for examples.

Select Protein database

Select Protein database in FASTA format. See sample_data folder in Preview program folder for examples.

Fixed modification options

You may provide fixed modifications. The pulldown menu for each edit box provides common modifications.  The user may also enter any modification not on the pulldown menu by typing the exact mass in the empty box.

Cysteine modification mass

Enter the mass in Daltons, of a fixed modification on Cysteine. In default mode (unselected), Preview will test for common modifications (0, 46, 57, 58, and 71).

Lysine, Arginine, N-terminal, and C-terminal modification masses

Enter the mass in Daltons of a fixed modification from the pulldown menu or typing in an exact mass. In default mode, Preview will assume 0 Da, and will not test for other possibilities.

Search Options

Digestion cleavage site(s) and side

Enter one-letter abbreviations for residues at cleavage points. Default is RK, meaning trypsin, with the cleavage side set to C-terminal side of the cleavage point.

Initial search specificity

Preview chooses representative proteins based on the initial search. Subsequent searches find modifications and non-specific digestions. Fully specific search (default) is recommended for digested samples. Fully specific (the default) means both peptide termini must agree with the input digestion cleavages. N-ragged search means that the C-terminus must agree, and C-ragged means that the N-terminus must agree. Semispecific means one terminus (either one) can disagree. Nonspecific means that both termini can disagree.

Phospho enriched

Check this box only if the sample is highly enriched in phosphopeptides, that is, the predominant composition is that of phosphopeptides.

Wildcard search

This option enables searches of the spectra with a wild-card modification, which allows any integer mass change (in the range of -50 to +120) to any one residue. The mass of the modification will be reported to the accuracy of the precursor mass.

Try all charge assignments

By default, Preview considers only the precursor charge assignments in the .dta or .mgf input, but selecting this option will force Preview to consider z = +1, +2, +3 for each CID spectrum, and z = +2, +3, +4 for each ETD spectrum. This may give better results for lower resolution ion-trap precursor scans.

Fragmentation type

Choose between CID / HCD (b and y ions) or ETD / ECD (c and z ions).

Recalibrate masses

Preview optionally creates a new MS/MS data file (.mgf format) in the results folder with recalibrated (1) precursors only, (2) fragments only, or (3) both precursors and fragments (default), or makes no recalibrated data file. The original file is not altered.

Additional Items of Note

Preferences

The Preferences dialog is located under the menu Edit > Preferences.  Use this to set the working folder for results. Resulting files such as recalibrated spectra and html results will be saved within the selected folder. Note that resulting files are never deleted; if desired to be purged, they must be removed manually.

Parameters load/save

For convenience, you can save and load your parameters, such as the modifications and digests. Note that a parameter file (params.prv) will be created for each run, located within the working folder.