Synapter report

Input

File nameNumber of features
Identification peptide:master.rds6699
Quantitation peptide:MSe_101111_25fmol_UPS1_in_Ecoli_03_IA_final_peptide.csv.gz10750
Quantitation Pep3D:MSe_101111_25fmol_UPS1_in_Ecoli_03_Pep3DAMRT.csv.gz50711
Fasta file:EcoliK12_enolase_UPSsimga_NB.fasta

Parameter nameValue
MasterTRUE
Peptide FDR0.01
Protein FPR0.01
Identification mass tolerance (ppm)20
Quantitation mass tolerance (ppm)20
Loess span (RT modelling)0.05
Filtering unique peptidesTRUE

Grid parameterValue
Mass tolerance (ppm) start7
Mass tolerance (ppm) end11
Mass tolerance (ppm) by1
Retention time stdev start1
Retention time stdev end6
Retention time stdev by1
Feature proportion 0.1
Number of features0
parameters selectionauto

Filtering

Peptide false discovery rate

Fig-pepScores.jpg
PepFrag1.RandomPepFrag1.RegularPepFrag2.RandomPepFrag2.Regular
2300772521322906

Fig-qValues.jpg

Mass tolerance

Fig-Ident-ppmError1.jpgFig-Quant-ppmError1.jpg

25%50%75%90%91%92%93%94%95%96%97%98%99%100%
Ident1.042.2914.1196.8657.2577.98.499.41811.22112.77915.32218.72621.92928.664
Quant0.4380.8961.562.3512.442.5392.672.9373.3263.8014.9836.2428.50422.896

Fig-Ident-ppmError2.jpgFig-Quant-ppmError2.jpg

25%50%75%90%91%92%93%94%95%96%97%98%99%100%
Ident1.0182.2384.0086.4066.737.037.5578.2268.83810.01611.99313.89316.29219.744
Quant0.4380.8941.5562.342.4342.5272.6432.9293.2733.724.7876.1138.0918.082

Retention time modelling

Retention time model

Fig-rtData.jpg
Fig-rtDiff.jpgFig-rtModel.jpg

25%50%75%90%91%92%93%94%95%96%97%98%99%100%
Retention time difference: 0.0060.0140.0260.0490.0540.0620.0750.1110.1540.3310.6512.5757.82643.64

Feature space

Fig-all-features.jpg
Fig-some-features.svg
Using nsd = 2 and ppm error = 10 as an example. Optimal values are selected below.

Grid optimisation

Using 10% of the data.
Grid imageFig-grid-total.jpgFig-grid-model.jpgFig-grid-details.jpg
Grid table
7891011
10.7330.7380.7430.7520.756
20.8140.8230.830.8390.842
30.8210.830.8350.8420.848
40.8040.8090.8090.8120.819
50.7730.7770.7770.7790.781
60.7520.7520.7540.7580.754
7891011
10.8330.8330.8330.8370.837
20.9240.9240.9240.9280.928
30.9280.9280.9280.9280.928
40.8950.8950.8950.8880.884
50.8480.8440.8440.8330.83
60.8150.8120.8120.8010.793
7891011
10.9790.9790.9790.9750.975
20.9810.9810.9810.9770.977
30.9770.9770.9770.9730.97
40.9840.9840.9840.980.976
50.9790.9830.9830.9790.983
60.9830.9870.9870.9820.982
Best value0.8480.9280.987
Best parameter(s)
ppmnsd
113
ppmnsd
73
83
93
102
103
112
113
ppmnsd
86
96

Grid details

Setting best grid parameters using 'auto':
- Mass tolerance (ppm): 8
- Number of retention time stdev: 3

EMRT matching

Fig-emrt-matching.jpg
0861
14698
278
31
44

Performance

(S) Synapter: 4698 EMRTs uniquely matched.
(I) Identification: 5642 peptides.
(Q) Quantitation: 2685 peptides.
Enrichment (S/Q): 74.97%
Overlap:
Q261
S2256
QS2424

Exported result files

Identification peptide file (non filtered)
Quantitation peptide file (non filtered)
Identification peptide file (filtered)
Quantitation peptide file (filtered)
Merged peptides (light)
Merged peptides (full)
Matched peptides (light)
Matched peptides (full)
Saved R object (binary)

Full analysis log

1Instance created on Mon Jun 25 09:44:45 2012
2Identification final peptide is a _master_ file.
3Read master identification peptide (rds) data [6699,70]
4Read quantitation peptide data [20986,64]
5Read quantitation Pep3D data [1195595,35]
6Filtered quantitation peptide by PepFrag1|2 [15193,64]
7Filtered quantitation Pep3D by Function [188568,35]
8Kept unique spectrum ids quantitation Pep3D [50711,35]
9Added identification statistics to quantitation data
10Filtered quantitation Random entries [10750,68]
11Kept quantitation non duplicated peptide sequences [10522,68]
12Kept identification non duplicated peptide sequences [6583,70]
13Kept identification peptides that match unique protein [5738,70]
14Kept quantitation peptides that match unique protein [9153,68]
15Set peptide score fdr to 0.01
16Filtered quantitation peptide data on pep score with fdr 0.01 [2690,68]
17Set quantitation ppm error to 20
18Quantitation mass error filtered at 20 ppm [2687,68]
19Set identification ppm error to 20
20Identification mass error filtered at 20 ppm [5645,70]
21Set protein fpr to 0.01
22Filtered identification peptide data using protein fpr 0.01 [5642,70]
23Set protein fpr to 0.01
24Filtered quantitation peptide data using protein fpr 0.01 [2685,68]
25Merged identification and quantitation data [2558,138]
26Set span to 0.05
27Modelled retention time using lowess and span 0.05
28Set nsd to 2
29Set ppm error to 10
30Performed grid search using 10% of identification peptides.
31Set 'nsd' and 'ppm error' to 3 and 8 (best 'auto')
32Matched identification peptides and quantitation EMRTs [5642,109]



(Page generated on Mon Jun 25 09:50:22 2012 by hwriter )