Biology Reference
In-Depth Information
Fig.
1
Flowchart of a SRM-MS project
Table 1
List of software tools mentioned in this chapter, including references, and short descriptions
Skyline [
4
]
Windows based client application supporting quantitative SRM-MS method
development and extensive analysis of resulting mass spectrometry data
SRM Collider [
5
]
Web service to detect and avoid shared transitions to increase precision of
SRM-MS measurements
http://www.srmcollider.org
MQuest/Mprophet [
6
] Web service to automatically score SRM-MS measurements using decoy
transitions and obtain false discovery rates (FDR)
http://www.mprophet.
2.2 SRM Peptide
assays
SRM-MS requires prior knowledge on the properties of peptides to
be monitored. This prior knowledge includes retention time as well as
fragmentation pattern of peptides obtained with a certain mass spec-
trometer. Either this prior knowledge is deposited in repositories such
as MR Maid [
7
], MASCP Gator [
8
], Promex [
9
], PASSEL [
10
] or
has to be determined prior to SRM-MS measurements take place.
Outlined below are common ways to obtain this prior knowledge.
2.2.1 Prior Knowledge of
Transitions: Repositories
Conventional low energy
collision-induced dissociation
(CID) ion-trap
fragmentation patterns of peptides of shotgun mass spectrometers are
often distinct from CID fragmentation pattern of the same peptide in
a beam type triple quadrupole mass spectrometer. For example, the
most intense fragment ions in CID mode are not necessarily the most
intense fragment ions in a triple quadrupole due to the differences in
energy transfer to the peptide found in resonance (ion-trap) versus
beam type (quadrupole) [
11
]. Recently, changes to instrumentation
have lead to the possibility of peptide fragmentation in a quadrupole
2.2.2
HCD shotgun
