---
title: "Fragment matching using *synapter*"
author:
- name: Laurent Gatto
  affiliation: Computational Proteomics Unit, Cambridge, UK.
- name: Sebastian Gibb
  affiliation: Department of Anesthesiology and Intensive Care, University Medicine Greifswald, Germany.
- name: Pavel V. Shliaha
  affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark.
package: synapter
abstract: >
  This vignette describes how to apply fragment matching to
  MS$^E$/HDMS$^E$ data using the 'synapter' package. The
  fragment matching feature allows one to rescue non unique matches
  and remove falsely assigned unique matches as well.
bibliography: synapter.bib
output:
  BiocStyle::html_document2:
    toc_float: true
    tidy: TRUE
vignette: >
  %\VignetteIndexEntry{Fragment matching using 'synapter'}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteKeywords{Mass Spectrometry, Proteomics, Bioinformatics, quantitative, Ion mobility, label-free}
  %\VignetteEncoding{UTF-8}
  %\VignettePackage{synapter}
---

```{r environment, echo=FALSE}
suppressPackageStartupMessages(library("synapter"))
suppressPackageStartupMessages(library("synapterdata"))
suppressPackageStartupMessages(library("BiocStyle"))
synobj2RData()
```

```{r include_forword, child="Foreword.md"}
```

```{r include_bugs, child="Bugs.md"}
```

# Introduction

This document assumes familiarity with standard `r Biocpkg("synapter")`
pipeline described in [@Bond2013] and in the package
`r Biocpkg("synapter")` vignette, available
[online](https://bioconductor.org/packages/release/bioc/vignettes/synapter/inst/doc/synapter.html)
and with `vignette("synapter", package = "synapter")`.

In this vignette we introduce a new fragment matching feature (see figures
[2](\#fig:plotfm22), [3](\#fig:plotfmseq) and [4](\#fig:plotfmid)) which
improves the matching of identification and the quantitation features. After
applying the usual `synergise1` workflow (see `?synergise1` and `?Synapter`
for details) a number of multiple matches and possible false unique matches
remain that can be deconvoluted by comparing common peaks in the identification
fragment peaks and the quantitation spectra.

The example data `synobj2` used throughout this document is available in the
`r Biocpkg("synapterdata")` package and can be directly load as follows:

```{r loadsynobj2, eval=FALSE}
library("synapterdata")
synobj2RData()
```

In the [next section](\sec:synergise] we describe how `synobj2` was generated.
The test files used in this vignette can be downloaded from
http://proteome.sysbiol.cam.ac.uk/lgatto/synapter/data/.
The following sections then describe the new fragment matching functionality.

# Running `synergise1`{#sec:synergise}

One has to run the `synergise1` workflow before fragment
matching can be applied. Please read the general `r Biocpkg("synapter")`
[vignette](https://bioconductor.org/packages/release/bioc/vignettes/synapter/inst/doc/synapter.html)
for the general use of `synergise1`.
The additional data needed for the fragment matching procedure are a
`final_fragment.csv` file for the identification run and a `Spectrum.xml` file
for the quantitation run.

```{r create-synobj2-file, echo=FALSE, comment=NA}
cat(readLines(system.file(file.path("scripts", "create_synobj2.R"),
                          package="synapterdata"), n=13), sep="\n")
```
```{r create_synobj2}
synobj2 <- synergise1(object=synobj2,
                      outputdir=tempdir())
```

# Filtering fragments{#sec:filtfrag}

This step is optional and allows one to remove low abundance fragments
in the spectra using `filterFragments`. Filtering fragments can remove noise
in the spectra and reduce undesired fragment matches. Prior to filtering, the
`plotCumulativeNumberOfFragments` function can be use to visualise the
intensity of all fragments. Both functions have an argument `what` to decide
what spectra/fragments to filter/plot. Choose `fragments.ident` for the
identification fragments and `spectra.quant` for the quantitation fragments.

```{r filterfragmentsplot, fig.cap="Cumulative Number of Fragments"}
plotCumulativeNumberOfFragments(synobj2,
                                what = "fragments.ident")
plotCumulativeNumberOfFragments(synobj2,
                                what = "spectra.quant")
```

```{r filterfragments}
filterFragments(synobj2,
                what = "fragments.ident",
                minIntensity = 70)
filterFragments(synobj2,
                what = "spectra.quant",
                minIntensity = 70)
```

# Fragment matching{#sec:fragmentmatching}

This method, named `fragmentMatching`, performs the matching of the
identification fragments vs the quantitation spectra and counts the number
of identical peaks for each combination.

Because the peaks/fragments in the spectra of one run will never be
numerically identical to these in another, a tolerance parameter has
to be set using the `setFragmentMatchingPpmTolerance` function.
Peaks/Fragments within this tolerance are treated as identical.

```{r fm}
setFragmentMatchingPpmTolerance(synobj2, 25)
fragmentMatching(synobj2)
```

The `plotFragmentMatching` function illustrates the details of this fragment
matching procedure. If it is called without any additional argument every
matched pair (fragment vs spectrum) is plotted.
One can use the `key` argument to select a special value in a column
(defined by the `column` argument) of the `MatchedEMRTs` `data.frame`.
E.g. if one wants to select the fragment matching results with a high number
of common peaks, e.g. 28 common peaks:

```{r plotfm22, fig.cap="Fragment matching for cases with 28 common fragments. The identification data are shown on the top (blue) and the quantitation data are on the bottom (red). Common peaks are displayed in darker colours and highlighted by full points."}
plotFragmentMatching(synobj2,
                     key = 28,
                     column = "FragmentMatching")
```

Or, if one is interested in all results for the peptide with the sequence
`"TALIDGLAQR"`.

```{r plotfmseq, fig.cap="Fragment matching for peptide *TALIDGLAQ*."}
plotFragmentMatching(synobj2,
                     key = "TALIDGLAQR",
                     column = "peptide.seq")
```

Maybe the peptide with a special precursor ID looks interesting.

```{r, plotfmid, fig.cap="Fragment matching precursor with *leID* identifier 12589."}
plotFragmentMatching(synobj2,
                     key = 12589,
                     column = "precursor.leID.ident")
```

# Plot distribution of common peaks{#sec:plotperf}

The `plotFragmentMatchingPerformance` function can be used to
assess the performance of the fragment matching and the result of the
filtering procedure (see below) based on the number of common
peaks. This function invisibly returns a list with matrices containing
true positive, false positive, true negative and false negative
matches for the unique and non unique matches EMRT matches, as
illustrated in tables [1](\#tab:confusionmatrixunique) and
[2](\#tab:confusionmatrixnonunqiue).
Both tables could be also generated by `fragmentMatchingPerformance`.

```{r plotfmperformance, fig.cap="Number of true/false match peptides for different peak matching thresholds and difference in number of peaks between the first and second (in terms of number of common peaks) possible matches. The former metric is used to filter out possible false positive unique matches while the second is used to filter multiple matches. Empty circles indicate zero peptides."}
m <- plotFragmentMatchingPerformance(synobj2)
```

```{r confusionmatrixunique, results="asis", echo=FALSE}
knitr::kable(m$unique[1:15,], row.names=FALSE,
             caption="Number of true positives, false negatives, false positives, false negatives and false discovery rate for a given number of common peaks.")
```

```{r confusionmatrixnonunqiue, results="asis", echo=FALSE}
knitr::kable(m$nonunique[1:15,], row.names=FALSE,
             caption="Number of true positives, false negatives, false positives, false negatives and false discovery rate for a given difference in number of common peaks between the higest and second highest multiply matching EMRTs in terms of number of common peptides.")
```

# Filtering unique matches{#sec:unique}

From the left panel on figure [7](\#fig:plotfmperformance) and table
[1](\#tab:confusionmatrixunique) displaying counts for unique matches one can
define filtering values for the unique (this section) and multiple matches
([next section](\#sec:nonunique)). In the case of uniquely matching EMRTs, one
can easily reduce the number of false matches by requiring that true matches
must have at least one peak/fragment in common. Clearly this will also
remove some true matches. The question is whether you want to rely on
matches that have no (or only a few) peaks/fragments in common?

```{r filerunique}
performance(synobj2)
getEMRTtable(synobj2)
filterUniqueMatches(synobj2, minNumber = 1)
performance(synobj2)
getEMRTtable(synobj2)
```

# Filtering non-unique matches{#sec:multiple}

The largest benefit of fragment matching is for non unique
matches. If we assume that true match have a highest number of common
peaks/fragments, we can distinguish correct matches among multiple
possible matches that could not resolved before (c.f. section
[\#sec:plotperf]). To do so, we use the difference of common peaks
from the highest to the second highest number in the match
group. Assuming two cases with multiple matches. In the first case, we
have two possible matches: a match with 7 and a match with 2 fragments
in common. In the second ambiguous match, there are a matches with 2
and 1 fragments in common respectively. If we decide to accept a
difference of at least 2, our first multiple match case be resolved
into a unique match as the difference between the best and second
matches is 5 and the best match with 7 common fragments will be
upgraded to a unique match.

The right panel of figure [7](\#fig:plotfmperformance) and table
[2](\#tab:confusionmatrixnonunqiue) can be used to choose a good threshold for
the difference in number of common peaks.

```{r filernonunique, echo=-1}
oldEMRTtable <- getEMRTtable(synobj2)
performance(synobj2)
getEMRTtable(synobj2)
filterNonUniqueMatches(synobj2, minDelta = 2)
performance(synobj2)
getEMRTtable(synobj2)
```

In this example we rescued `r getEMRTtable(synobj2)["1"]-oldEMRTtable["1"]` unique
matches out of the non unique ones.

# Exporting results

Like in the initial `r Biocpkg("synapter")` workflow, it is possible to export the
`MatchedEMRT` results using the `writeMatchedEMRTs` function. The table has
some new columns that correspond to the fragment matching procedure,
e.g. `FragmentMatching`, \ldots.

```{r export, eval=FALSE}
writeMatchedEMRTs(synobj2, file = "MatchedEMRTs.csv")
```

# Session information{#sec:sessionInfo}

All software and respective versions used to produce this document are
listed below.

```{r sessioninfo}
sessionInfo()
```

# References
