DIA / SWATH Peptide identification & Quantification
DETAILS Raw file (.wiff or .raw) Msconvert (?AB Sciex converter)
DDA DDA or DIA?
mzML
DIA (SWATH)
TPP TPP or other?
msconvert & indexmzXML (TPP)
mzXML
TPP Search (xTandem, Comet)
OTHER idconvert? (TPP)
alternative search engine
swaths. txt OpenSwathWorkflow (openMS)
PeptideProphet Xinteract (TPP)
pep.xml
interact. pep.xml
Assay_library _con_irt.tsv
YES
interact. pep.xml
iRT. TraML InterProphetParser (TPP)
output .tsv
Multiple searches?
NO
interact. iprophet .pep.xml
Run Mayu?
YES pyprophet (python)
NO
Mayu.pl (TPP)
.csv
output_ qvalue .tsv
YES output_ qvalue .tsv
P=0.9??
.splib
Spiked or endogenous iRT peptides?
CiRTs
Multi-file experiment?
endo.
PEPTIDE:iRT, …
-k ? other iRT refs?
NO
spiked
SpectraST (TPP)
spectrast2spectrast _iRT.py (python) default is spiked SiRT’s _irt.splib
feature_alignment.py (python)
SWATH peptide IDs with quantitation and q-values
Add Tools or Wrappers to the following site: https://github.com/galaxyproteomics/tools-galaxyp/issues/10
Assay_library _con_irt.tsv
spectrast2tsv.py (python)
_con_irt .splib
SpectraST -cAC (TPP)
1
MODULE 2
Raw file (.wiff or .raw) Msconvert (?AB Sciex converter)
DDA DDA or DIA?
mzML
TPP TPP or other?
2 msconvert & indexmzXML (TPP)
mzXML
TPP Search (xTandem, Comet)
PeptideProphet Xinteract (TPP)
pep.xml
OTHER idconvert? (TPP)
alternative search engine
interact. pep.xml
2 DIA (SWATH)
(openMS)
InterProphetParser (TPP)
Run Mayu?
YES NO
Mayu.pl (TPP)
.csv
output .tsv output_ qvalue .tsv
output_ qvalue .tsv
Multiple searches?
NO
interact. iprophet .pep.xml
_con_irt.tsv
iRT. pyprophet TraML (python)
YES
YES
interact. pep.xml
• Can PeptideShaker be seen as an alternative either to generate any of the intermediate steps swaths. or as an input for txt SpectraST? - Can mzidentml be converted to pepxml? OpenSwathWorkflow Assay_library
P=0.9??
.splib
Spiked or endogenous iRT peptides?
CiRTs
Multi-file experiment?
endo.
PEPTIDE:iRT, …
-k ? other iRT refs?
NO
spiked
SpectraST (TPP)
spectrast2spectrast _iRT.py (python) default is spiked SiRT’s _irt.splib
This makes it impossible to update clones. When this happens, ... versions of the Yocto kernel (from the Yocto repository, or the Intel Github repositories on ...
Switch system is mobile Cashier backend sale system for merchants, which provides the following base features: Management of Partners, Merchants, Users, Cashiers, Cash registers, mPOS Terminals and Merchant's Product catalogues. Processing Sales with
Aug 7, 2012 - app ear in a tub e formula similar to the one defining the intrinsic volumes. Intrinsic volumes of convex cones. Random convex p ograms. Lo calizing ...... β. /2). =: M n. ,β. Intrinsic volumes of convex cones. Measures of th e semide
complex life cycle in their mosquito vector and vertebrate hosts. .... their host cells to guarantee the safe delivery of mer- ... for parasite identification http://www.
Tree Outline â Sketching â Dimensions â Diameter. ⢠Specify diameter of top circle to be 5 mm. ⢠Note that all circles should change diameter at this time. Play around with this a little, enjoy yourself. 13. Create bolt holes. ⢠Toolbar â
This document documents a new format for Heathkit H17 Hard-sectored Disk Images. The current format being used, âH8Dâ, does not preserve the header ...
Elasticity. Unit 2. -Elasticity of Demand. -Elasticity of Supply. 76-89. October 5. (19). Income Elasticity. Cross-Price Elasticity. Taxes. Unit 2. -Income and Cross ...
May 11, 2017 - 1. Coast Guard. Central Intelligence Agency. Army. Navy. Air Force. National ... We emphasize technical excellence & technical truth ...
With U-Boot as the boot loader, the above need to be put into a format that U-Boot understands. The following describes using the FIT format (see doc/uImage.
The GS1 barcode is how we base everything off of. When you put the. capability of a consumer to suddenly find out specifics, you might find out that they actually ...
The game is set in a re imagined version of modern day Manchester, but with a .... piles of shipping crates in this location are the subject of another Photo Op,.
market. This overview paper outlines in detail the concept and planning behind Electroneum ... listed on the London Stock Exchange, Mark .... 3G or 4G data.
Just the Linux kernel. ⢠Linux and the device tree. ⢠Linux, the device tree, and a root file system. The simulator only supports using separate images for Linux ...
calculated as the amount of resources used to produce a product or service. It refers to the ..... Managers scan their environment for information that may affect ...
Everyone will then have an opportunity to take a break, get some refreshments and a breath of air for a few minutes. During the second hour, the Facilitator will ...
convention for a custom branch is custom-[organization domain]. For example custom- ccvonline. It is up to each of those organizations to determine how their ...
