Input

Files

File name Number of features
Identification peptide: 01_HDMSe_tiny.csv 4979
Quantitation peptide: 02_MSe_tiny.csv 3492
Quantitation Pep3D: 03_Pep3D_tiny.csv 8356
Fasta file: 04_test_database.fasta

General Parameters

Parameter name Value
Master FALSE
Peptide FDR 0.01
Protein FPR 0.01
Peptide Length 7
Missed cleavages 0
Isoleucin equals Leucin FALSE
Identification mass tolerance (ppm) 20
Quantitation mass tolerance (ppm) 20
Loess span (RT modelling) 0.05
Filtering unique peptides TRUE

Grid Search Parameters

Grid parameter Value
Mass tolerance (ppm) start 2
Mass tolerance (ppm) end 20
Mass tolerance (ppm) by 2
Retention time stdev start 0.5
Retention time stdev end 5
Retention time stdev by 0.5
Feature proportion 0.2
Number of features 0
parameters selection auto

Filtering

Peptide False Discovery Rate

Peptide Scores

Peptide Numbers

PepFrag1.Random PepFrag1.Regular PepFrag2.Random PepFrag2.Regular
ident 256 3522 448 1393
quant 496 2664 500 745

Peptide FDR

Mass tolerance

25% 50% 75% 90% 91% 92% 93% 94% 95% 96% 97% 98% 99% 100%
Ident 0.982 2.183 4.070 6.750 7.663 8.299 9.136 9.989 12.060 13.997 16.082 19.288 22.496 28.664
Quant 0.432 0.972 1.682 3.083 3.341 3.606 3.992 5.021 5.733 6.455 7.736 9.124 14.897 24.599

25% 50% 75% 90% 91% 92% 93% 94% 95% 96% 97% 98% 99% 100%
Ident 0.968 2.144 3.939 6.233 6.589 7.035 7.942 8.775 9.523 10.688 12.643 14.563 17.007 19.744
Quant 0.430 0.962 1.662 3.008 3.202 3.413 3.843 4.407 5.239 6.103 7.162 8.261 9.548 19.817

Retention Time Modelling

Retention Time Model

25% 50% 75% 90% 91% 92% 93% 94% 95% 96% 97% 98% 99% 100%
Retention time difference: 0.003 0.008 0.016 0.029 0.031 0.034 0.04 0.047 0.057 0.072 0.463 4.161 10.703 32.14

Feature Space

Using nsd = 2 and ppm error = 10 as an example.<br />Optimal values are selected below.

Using nsd = 2 and ppm error = 10 as an example.
Optimal values are selected below.

Grid Optimisation

Using 20% of the data.

plotGrid(obj, what=“details”)

Grid Tables

total

Image

Table
2 4 6 8 10 12 14 16 18 20
0.5 0.406 0.479 0.489 0.494 0.496 0.496 0.496 0.496 0.496 0.496
1 0.609 0.721 0.742 0.750 0.752 0.752 0.752 0.752 0.752 0.752
1.5 0.645 0.768 0.793 0.805 0.808 0.808 0.808 0.808 0.808 0.808
2 0.649 0.772 0.796 0.808 0.811 0.811 0.811 0.811 0.811 0.811
2.5 0.649 0.772 0.796 0.808 0.811 0.811 0.811 0.811 0.811 0.811
3 0.649 0.772 0.796 0.808 0.811 0.811 0.811 0.811 0.811 0.811
3.5 0.649 0.772 0.796 0.808 0.811 0.811 0.810 0.810 0.810 0.810
4 0.649 0.772 0.796 0.808 0.811 0.811 0.810 0.810 0.810 0.810
4.5 0.650 0.773 0.798 0.810 0.811 0.811 0.808 0.808 0.808 0.808
5 0.650 0.773 0.796 0.808 0.810 0.810 0.806 0.806 0.806 0.806

Best Grid Value total: 0.8111658

nsd ppm imdiff
2.0 10 Inf
2.5 10 Inf
3.0 10 Inf
3.5 10 Inf
4.0 10 Inf
4.5 10 Inf
2.0 12 Inf
2.5 12 Inf
3.0 12 Inf
3.5 12 Inf
4.0 12 Inf
4.5 12 Inf
2.0 14 Inf
2.5 14 Inf
3.0 14 Inf
2.0 16 Inf
2.5 16 Inf
3.0 16 Inf
2.0 18 Inf
2.5 18 Inf
3.0 18 Inf
2.0 20 Inf
2.5 20 Inf
3.0 20 Inf

model

Image

Table
2 4 6 8 10 12 14 16 18 20
0.5 0.505 0.578 0.578 0.581 0.581 0.581 0.581 0.581 0.581 0.581
1 0.761 0.865 0.869 0.872 0.872 0.872 0.872 0.872 0.872 0.872
1.5 0.813 0.931 0.934 0.941 0.941 0.941 0.941 0.941 0.941 0.941
2 0.820 0.938 0.941 0.948 0.948 0.948 0.948 0.948 0.948 0.948
2.5 0.820 0.938 0.941 0.948 0.948 0.948 0.948 0.948 0.948 0.948
3 0.820 0.938 0.941 0.948 0.948 0.948 0.948 0.948 0.948 0.948
3.5 0.820 0.938 0.941 0.948 0.948 0.948 0.945 0.945 0.945 0.945
4 0.820 0.938 0.941 0.948 0.948 0.948 0.945 0.945 0.945 0.945
4.5 0.820 0.938 0.941 0.948 0.945 0.945 0.941 0.941 0.941 0.941
5 0.820 0.938 0.938 0.945 0.941 0.941 0.938 0.938 0.938 0.938

Best Grid Value model: 0.9480969

nsd ppm imdiff
2.0 8 Inf
2.5 8 Inf
3.0 8 Inf
3.5 8 Inf
4.0 8 Inf
4.5 8 Inf
2.0 10 Inf
2.5 10 Inf
3.0 10 Inf
3.5 10 Inf
4.0 10 Inf
2.0 12 Inf
2.5 12 Inf
3.0 12 Inf
3.5 12 Inf
4.0 12 Inf
2.0 14 Inf
2.5 14 Inf
3.0 14 Inf
2.0 16 Inf
2.5 16 Inf
3.0 16 Inf
2.0 18 Inf
2.5 18 Inf
3.0 18 Inf
2.0 20 Inf
2.5 20 Inf
3.0 20 Inf

details

Image

Table
2 4 6 8 10 12 14 16 18 20
0.5 1.000 0.994 0.988 0.988 0.988 0.988 0.988 0.988 0.988 0.988
1 0.991 0.984 0.980 0.977 0.977 0.977 0.977 0.977 0.977 0.977
1.5 0.992 0.985 0.982 0.978 0.978 0.978 0.978 0.978 0.978 0.978
2 0.992 0.985 0.982 0.979 0.979 0.979 0.979 0.979 0.979 0.979
2.5 0.992 0.985 0.982 0.979 0.979 0.979 0.979 0.979 0.979 0.979
3 0.992 0.985 0.982 0.979 0.979 0.979 0.979 0.979 0.979 0.979
3.5 0.992 0.985 0.982 0.979 0.979 0.979 0.978 0.978 0.978 0.978
4 0.992 0.985 0.982 0.979 0.979 0.979 0.978 0.978 0.978 0.978
4.5 0.988 0.982 0.978 0.975 0.975 0.975 0.975 0.975 0.975 0.975
5 0.988 0.982 0.978 0.975 0.975 0.975 0.975 0.975 0.975 0.975

Best Grid Value details: 1

nsd ppm imdiff
0.5 2 Inf

Grid Details

nsd ppm -2 -1 0 1 2
0.5 2 0 0 143 146 0
0.5 4 0 1 121 167 0
0.5 6 0 2 120 167 0
0.5 8 0 2 119 168 0
0.5 10 0 2 119 168 0
0.5 12 0 2 119 168 0
0.5 14 0 2 119 168 0
0.5 16 0 2 119 168 0
0.5 18 0 2 119 168 0
0.5 20 0 2 119 168 0
1 2 0 2 67 220 0
1 4 0 4 35 250 0
1 6 0 5 33 251 0
1 8 0 6 31 252 0
1 10 0 6 31 252 0
1 12 0 6 31 252 0
1 14 0 6 31 252 0
1 16 0 6 31 252 0
1 18 0 6 31 252 0
1 20 0 6 31 252 0
1.5 2 0 2 52 235 0
1.5 4 0 4 16 269 0
1.5 6 0 5 14 270 0
1.5 8 0 6 11 272 0
1.5 10 0 6 11 272 0
1.5 12 0 6 11 272 0
1.5 14 0 6 11 272 0
1.5 16 0 6 11 272 0
1.5 18 0 6 11 272 0
1.5 20 0 6 11 272 0
2 2 0 2 50 237 0
2 4 0 4 14 271 0
2 6 0 5 12 272 0
2 8 0 6 9 274 0
2 10 0 6 9 274 0
2 12 0 6 9 274 0
2 14 0 6 9 274 0
2 16 0 6 9 274 0
2 18 0 6 9 274 0
2 20 0 6 9 274 0
2.5 2 0 2 50 237 0
2.5 4 0 4 14 271 0
2.5 6 0 5 12 272 0
2.5 8 0 6 9 274 0
2.5 10 0 6 9 274 0
2.5 12 0 6 9 274 0
2.5 14 0 6 9 274 0
2.5 16 0 6 9 274 0
2.5 18 0 6 9 274 0
2.5 20 0 6 9 274 0
3 2 0 2 50 237 0
3 4 0 4 14 271 0
3 6 0 5 12 272 0
3 8 0 6 9 274 0
3 10 0 6 9 274 0
3 12 0 6 9 274 0
3 14 0 6 9 274 0
3 16 0 6 9 274 0
3 18 0 6 9 274 0
3 20 0 6 9 274 0
3.5 2 0 2 50 237 0
3.5 4 0 4 14 271 0
3.5 6 0 5 12 272 0
3.5 8 0 6 9 274 0
3.5 10 0 6 9 274 0
3.5 12 0 6 9 274 0
3.5 14 1 6 9 273 0
3.5 16 1 6 9 273 0
3.5 18 1 6 9 273 0
3.5 20 1 6 9 273 0
4 2 0 2 50 237 0
4 4 0 4 14 271 0
4 6 0 5 12 272 0
4 8 0 6 9 274 0
4 10 0 6 9 274 0
4 12 0 6 9 274 0
4 14 1 6 9 273 0
4 16 1 6 9 273 0
4 18 1 6 9 273 0
4 20 1 6 9 273 0
4.5 2 0 3 49 237 0
4.5 4 0 5 13 271 0
4.5 6 0 6 11 272 0
4.5 8 0 7 8 274 0
4.5 10 1 7 8 273 0
4.5 12 1 7 8 273 0
4.5 14 2 7 8 272 0
4.5 16 2 7 8 272 0
4.5 18 2 7 8 272 0
4.5 20 2 7 8 272 0
5 2 0 3 49 237 0
5 4 0 5 13 271 0
5 6 1 6 11 271 0
5 8 1 7 8 273 0
5 10 2 7 8 272 0
5 12 2 7 8 272 0
5 14 3 7 8 271 0
5 16 3 7 8 271 0
5 18 3 7 8 271 0
5 20 3 7 8 271 0

Best Grid Parameters

Setting best grid parameters using ‘auto’

  • Mass tolerance (ppm): 8
  • Number of retention time stdev: 2

EMRT Matching

Number of assigned EMRTs Freq
0 539
1 2506

Performance

Enrichment

group values
(S) Synapter (uniquely matched EMRTs) 2506
(I) Identification 3045
(Q) Quantitation 1840
(S/Q) Enrichment 36.2%

Overlap

Number of peptides
Q 433
S 1097
QS 1407

Source

Number of peptides with valid counts Number of NA
rescue 5 29
transfer 2506 505

Full Analysis Log

  • Instance created on Wed Jun 6 23:37:36 2012
  • Read identification peptide data [5915,18]
  • Read quantitation peptide data [4731,17]
  • Read quantitation Pep3D data [8356,10]
  • Filtered identification peptide by PepFrag1|2 [5684,18]
  • Filtered quantitation peptide by PepFrag1|2 [4492,17]
  • Filtered quantitation Pep3D by Function [8356,10]
  • Kept unique spectrum ids quantitation Pep3D [8356,10]
  • Added identification statistics to quantitation data
  • Filtered quantitation Random entries [3492,21]
  • Added identification statistics to identification data
  • Filtered identification Random entries [4979,22]
  • Instance updated to synapter 1.99.0 on Sun Oct 16 16:47:24 2016
  • Kept quantitation non duplicated peptide sequences [3327,21]
  • Kept identification non duplicated peptide sequences [4852,22]
  • Kept identification peptides that match unique protein (0 missed cleavages; I/L treatment: I != L) [3726,22]
  • Kept quantitation peptides that match unique protein (0 missed cleavages; I/L treatment: I != L) [2279,21]
  • Keeping quant peptides of length >= 7 [2105,21]
  • Keeping ident peptides of length >= 7 [3545,22]
  • Set peptide score fdr to 0.01
  • Filtered quantitation peptide data on pep score with fdr 0.01 [1860,21]
  • Filtered identification peptide data on pep score with fdr 0.01 [3097,22]
  • Set quantitation ppm error to 20
  • Quantitation mass error filtered at 20 ppm [1849,21]
  • Set identification ppm error to 20
  • Identification mass error filtered at 20 ppm [3045,22]
  • Set protein fpr to 0.01
  • Filtered identification peptide data using protein fpr 0.01 [3045,22]
  • Set protein fpr to 0.01
  • Filtered quantitation peptide data using protein fpr 0.01 [1840,21]
  • Merged identification and quantitation data [1456,44]
  • Set span to 0.05
  • Modelled retention time using lowess and span 0.05
  • Set nsd to 2
  • Set ppm error to 10
  • Performed grid search using 20% of identification peptides.
  • Set ‘nsd’, ‘ppm error’ and ‘im diff’ to 2, 8 and Inf (best ‘auto’)
  • Matched identification peptides and quantitation EMRTs [3045,37]
  • Rescue EMRTs [3045,37] (rescue)

Session Info

## R version 3.5.1 Patched (2018-08-16 r75161)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 14.04.5 LTS
## 
## Matrix products: default
## BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
## LAPACK: /usr/lib/lapack/liblapack.so.3.0
## 
## locale:
##  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
##  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
##  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] parallel  stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
## [1] synapter_2.5.2      MSnbase_2.7.4       ProtGenerics_1.12.0
## [4] BiocParallel_1.14.2 mzR_2.15.2          Rcpp_0.12.18       
## [7] Biobase_2.40.0      BiocGenerics_0.26.0
## 
## loaded via a namespace (and not attached):
##  [1] httr_1.3.1            vsn_3.48.1            splines_3.5.1        
##  [4] foreach_1.4.4         assertthat_0.2.0      highr_0.7            
##  [7] affy_1.58.0           stats4_3.5.1          yaml_2.2.0           
## [10] impute_1.54.0         highlight_0.4.7.2     pillar_1.3.0         
## [13] backports_1.1.2       lattice_0.20-35       glue_1.3.0           
## [16] limma_3.36.3          digest_0.6.16         RColorBrewer_1.1-2   
## [19] XVector_0.20.0        qvalue_2.12.0         colorspace_1.3-2     
## [22] Matrix_1.2-14         htmltools_0.3.6       preprocessCore_1.42.0
## [25] plyr_1.8.4            devtools_1.13.6       MALDIquant_1.18      
## [28] XML_3.98-1.16         pkgconfig_2.0.2       zlibbioc_1.26.0      
## [31] purrr_0.2.5           scales_1.0.0          whisker_0.3-2        
## [34] affyio_1.50.0         cleaver_1.18.0        tibble_1.4.2         
## [37] IRanges_2.14.11       ggplot2_3.0.0         withr_2.1.2          
## [40] lazyeval_0.2.1        cli_1.0.0             survival_2.42-6      
## [43] magrittr_1.5          crayon_1.3.4          memoise_1.1.0        
## [46] evaluate_0.11         fs_1.2.6              doParallel_1.0.11    
## [49] MASS_7.3-50           xml2_1.2.0            BiocInstaller_1.30.0 
## [52] tools_3.5.1           hms_0.4.2             stringr_1.3.1        
## [55] S4Vectors_0.18.3      munsell_0.5.0         bindrcpp_0.2.2       
## [58] Biostrings_2.48.0     pcaMethods_1.72.0     compiler_3.5.1       
## [61] pkgdown_1.1.0         mzID_1.18.0           rlang_0.2.2          
## [64] grid_3.5.1            rstudioapi_0.7        iterators_1.0.10     
## [67] rmarkdown_1.10        testthat_2.0.0        gtable_0.2.0         
## [70] codetools_0.2-15      multtest_2.36.0       rematch_1.0.1        
## [73] roxygen2_6.1.0        curl_3.2              reshape2_1.4.3       
## [76] R6_2.2.2              knitr_1.20            dplyr_0.7.6          
## [79] bindr_0.1.1           commonmark_1.5        rprojroot_1.3-2      
## [82] readr_1.1.1           desc_1.2.0            stringi_1.2.4        
## [85] tidyselect_0.2.4