Version 27/07/2010
What is QuickMod?
QuickMod is a spectral library search based MSMS data analysis tool, designed to identify modified peptides.
A spectral library is a database of already identified MSMS spectra. Typically a peptide entry in the library is represented by a consensus spectrum; an averaged spectrum compiled from multiple, same precursor charge state, spectra representing the same peptide species.
The QuickMod algorithm assumes that the precursor mass difference between a query spectrum and a candidate library spectrum can be explained by a modification. Based on this assumption the two spectra are aligned and a list of similarity measures calculated. In a second step the most likely attachment position of the modification is determined.
The QuickMod scoring scheme was developed by carefully examining and combining various peak intensity and peak coverage based scoring features. Using a similar approach proposed for the Percolator algorithm (Käll et al., Nature Methods 2007, The optimal linear combination of the list of scoring features is derived using a Support Vector Machine classification algorithm).
QuickMod provides efficient means to evaluate the quality of a MS/MS dataset by revealing modifications induced by sample handling and preparation such as oxidation, pyro-Glu and salt adducts. More importantly, the search algorithm is capable of identifying known PTMs while suggesting a list of previously unknown or unexpected PTMs, to be verified in targeted experiments.
Currently, QuickMod only accepts spectra in Mascot Generic Format (MGF).
Please have a look here for a general description of this format.
In the « Data file content » area, one can directly paste a list of spectra in MGF.
In a test purpose, one can also load an example spectrum corresponding to this peptide/modification: M({15.999})PcAEDYLSVVLNQLcVLHEK
The spectral libraries available in this web-interface version of QuickMod were built by S. Stein at NIST; more information and related software can be found at peptide.nist.gov.
| Library | Spectra | Release date | Detailed content |
| Human Ion-Trap | 345 489 | 14/01/2010 | http://peptide.nist.gov/info/human.php |
| Human QTOF | 14 827 | 02/03/2010 | http://peptide.nist.gov/info/human_qtof.php |
| Human Serum Albumin, Ion-Trap | 2 309 | 03/08/2009 | http://peptide.nist.gov/info/hsa.php |
| Yeast Ion-Trap | 90 507 | 19/10/2009 | http://peptide.nist.gov/info/yeast.php |
| Yeast QTOF | 2 418 | 25/11/2009 | http://peptide.nist.gov/info/yeast_qtof.php |
Precursor mass tolerance
Allowed deviation (in m/z) between the precursor mass from the spectrum and the mass of candidate peptides from the database.
Fragment mass tolerance
Specify an error tolerance (in m/z) for MS/MS fragment ion mass values.
Modification mass tolerance
Additional allowed mass tolerance for modifications.
Number of candidates per spectrum
Number of possible results proposed by QuickMod for each spectrum.
Score threshold
Only results above this value will be displayed in the output. Recommended value is 0.6. More details on the score can be found here.
Your E-mail adress
If filled, the result will be sent to this e-mail adress.
Example: M({15.999})PcAEDYLSVVLNQLcVLHEK
({15.999}) : indicates a modification of approximatively 16 Da on Methionine
c (lower case) : the query spectrum was matched to a library spectrum representing a peptide with a Cys-Cam modification.
The current web-interface version of QuickMod calculates the similarity between a query spectrum and its spectral library candidates using a cross-correlation like scoring function. Similarity scores range from 0-1;
Approximate score interpretation
dp = 0 - no similarity
dp < 0.6 - unlikely match
dp 0.6 > dp > 0.8 - good match
dp >0.8 - excellent match
dp = 1 - perfect match
Any further question can be adressed to the ExPASy helpdesk.