SRM Collider
version 1.4
Hannes Röst 2012

Instructions

Transition Input

The main content is provided in the big textarea where peptides or transitions can be posted. There are three ways to provide input to the SRMCollider:

1) Peptide Sequences

You can provide one peptide sequence per line. The collider will then compute the precursor mass and the b and y series fragment masses and search for interferences. This may not be suited for you if you already have library fragment ion intensities.

2) MGF / SpectaST Style library

To assess the uniqueness of a specific assay, you can provide assays in SpectraST style format

Name: NLQGSNGGYAWEDEIK
Charge: 2
1167.53227 10 y10 1
890.42602 12 y7 1
504.26700 1 y4 1
962.43323 4 b10 1

This will then also allow you to study the uniqueness of the top n transitions.

3) CSV format

Alternatively, you can enter your transitions in CSV format. Each peptide precursor needs to have a unique identifier (UniquePeptideIdentifier) in this format, this can be a number or a combination of sequence, charge state and modification status. Please use the following column order (please do not provide a header):

UniquePeptideIdentifier, PrecursorPeptideSequence, PrecursorCharge, Q1Mass, Q3Mass, FragmentIonLibraryIntensity, FragmentIonCharge, FragmentIonAnnotation

For example, this is a valid input (note: no header)

tr1_1,NLQGSNGGYAWEDEIK,2,890.91106,1167.53227,10,1,y10
tr1_1,NLQGSNGGYAWEDEIK,2,890.91106,890.42602,12,1,y7
tr1_1,NLQGSNGGYAWEDEIK,2,890.91106,504.26700,1,1,y4
tr1_1,NLQGSNGGYAWEDEIK,2,890.91106,962.43323,4,1,b10
tr1_2,NLQGSNGGYAWEIK,2,890.91106,992.43323,4,1,b10
tr1_2,NLQGSNGGYAWEDIK,2,890.91106,982.43323,4,1,b10

Available Modifications

Currently, the SRMCollider understands the following modifications:

Further Options

Currently, a limited number of genomes are available, upon request more can be added. Please contact me at roest <> at <> imsb.ethz.ch

Precursor isotopes are considered in the analysis (but not fragment isotopes) and the default value is to consider isotopes up to +3 amu.