xiSPEC: web-based visualization, analysis and sharing of proteomics data [original]

Published online 8 May 2018 Nucleic Acids Research, 2018, Vol. 46, Web Server issue W473–W478

doi: 10.1093/nar/gky353

xiSPEC: web-based visualization, analysis and

sharing of proteomics data

Lars Kolbowski1,2, Colin Combe1and Juri Rappsilber1,2,*

1Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK

and 2Bioanalytics, Institute of Biotechnology, Technische Universit¨

at Berlin, 13355 Berlin, Germany

Received February 17, 2018; Revised April 17, 2018; Editorial Decision April 21, 2018; Accepted April 24, 2018

ABSTRACT

We present xiSPEC, a standard compliant, next-

generation web-based spectrum viewer for visu-

alizing, analyzing and sharing mass spectrome-

try data. Peptide-spectrum matches from standard

proteomics and cross-linking experiments are sup-

ported. xiSPEC is to date the only browser-based tool

supporting the standardized file formats mzML and

mzIdentML defined by the proteomics standards ini-

tiative. Users can either upload data directly or select

files from the PRIDE data repository as input. xiSPEC

allows users to save and share their datasets publicly

or password protected for providing access to col-

laborators or readers and reviewers of manuscripts.

The identification table features advanced interaction

controls and spectra are presented in three inter-

connected views: (i) annotated mass spectrum, (ii)

peptide sequence fragmentation key and (iii) qual-

ity control error plots of matched fragments. High-

lighting or selecting data points in any view is rep-

resented in all other views. Views are interactive

scalable vector graphic elements, which can be ex-

ported, e.g. for use in publication. xiSPEC allows for

re-annotation of spectra for easy hypothesis testing

by modifying input data. xiSPEC is freely accessi-

ble at http://spectrumviewer.org and the source code

is openly available on https://github.com/Rappsilber-

Laboratory/xiSPEC.

INTRODUCTION

Mass spectra are the foundation of proteomics. Their anal-

ysis leads to identifications of peptides which in turn iden-

tify the proteins present in the sample (1,2). In the case

of cross-linking experiments, linkage sites within the pep-

tides are also identified (3,4). This provides proximity in-

formation for pairs of amino acid residues which can elu-

cidate native protein structures (5) or protein–protein net-

works (6,7). In modern proteomics experiments thousands

of spectra are generated, which necessitates automated al-

gorithmic matching of spectra (search software). Neverthe-

less, humans still must be able to interact with spectra to

remain in control of the identification process and investi-

gate alternative hypotheses to those returned by automatic

processing.

A typical proteomics dataset consists of two types of

data: (i) mass spectra with associated data and (ii) pep-

tides matched to the spectra by the search software. Both

of these can come in different file formats depending on

the manufacturer of the instrument or the developers of

the search software, respectively. The multitude of file for-

mats lead to an initiative for creating standardized for-

mats for proteomics/mass spectrometry data by the Hu-

man Proteome Organization Proteomics Standards Initia-

tive (HUPO-PSI). The HUPO-PSI standard format for en-

coding raw spectrometer output is mzML (8), with tools

such as Proteowizard’s MSconvert (9) being available to

convert virtually every mass spectrometry raw data format

to mzML. The existing HUPO-PSI standard format for re-

porting identifications mzIdentML (10) has recently been

updated to version 1.2.0 (11), adding support for cross-

linking data. A variety of tools have been developed to con-

vert legacy formats to mzIdentML (9,12,13).

We strongly encourage the shift toward the use of com-

munity wide consistent standard formats. Therefore xiS-

PEC is fully compliant with the newest PSI standard for-

mats mzML and mzIdentML. To provide backward com-

patibility, we additionally support the still widely used Mas-

cot Generic Format (MGF) (14) for peak list data and iden-

tifications in a comma-separated format. To the best of our

knowledge, the only existing PSI compliant tool for view-

ing and analyzing spectra is PRIDE Inspector (15), which

has the downside of requiring download prior to use. It does

not currently support cross-link data, is not designed for hy-

pothesis testing by modifying the peptide-spectrum match

data and does not provide scalable vector graphic (SVG)

output. Proteomics data including cross-links can be visu-

alized and shared through the browser-based MS-Viewer

(16). However, MS-Viewer lacks support for the PSI stan-

dard identifications format (mzIdentML) and the ameni-

ties of modern web development. Lorikeet (https://github.

*To whom correspondence should be addressed. Tel: +49 30 314 72374; Email: juri.ra[email protected]

The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which

permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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W474 Nucleic Acids Research, 2018, Vol. 46, Web Server issue

com/UWPR/Lorikeet) is used for spectrum visualization in

proXL (17), a web-based platform for the analysis of cross-

linking data. Lorikeet is equivalent in functionality to MS-

Viewer, but with the benefit of being open source.

xiSPEC version 1.0 (website and sourceforge release

2012) is a stand alone browser-based spectrum viewer that

allows interrogating single spectra and their interpretation

in interconnected views with SVG output for figure making.

It has replaced the original Mascot spectrum viewer since

Mascot v. 2.5. We present here xiSPEC version 2.0, an inter-

active tool for visualizing and analyzing mass spectrometry

data in the browser. It supports data from standard pro-

teomics and cross-linking experiments. The interactive de-

sign of xiSPEC follows the principle of multiple coordinated

views (18). The user has all information available on a sin-

gle web page and all views of the data are interconnected.

We hope that xiSPEC’s ease of use will positively impact on

the proteomics community by enhancing data interrogation

and sharing.

IMPLEMENTATION

Essential to all the previously mentioned spectrum visual-

ization tools is the ability to associate fragments of peptide

sequences with peaks in the spectra. There are three ways

the annotation of peaks with corresponding peptide frag-

ments could occur. First, the annotated fragments could

be recorded in the mzIdentML file, the specification al-

lows for this. This has the benefit of allowing the spec-

trum viewer to show exactly those annotations that the

search software used to derive the identification. Never-

theless, most search software do not include this informa-

tion as it causes datasets to grow substantially. MS-Viewer

and Lorikeet use an alternative approach by incorporat-

ing the annotation process into the spectrum viewer. At

last, spectrum visualization and annotation can be sepa-

rated into separate software components or services. This

provides uniform annotation, separates concerns, eases the

maintenance of both the annotation and visualization tools

and allows the use of both independent of each other. An

example of a stand-alone annotator is PRIDE-asap (19).

PRIDE-asap does not support cross-linked peptides. There-

fore, we use xiAnnnotator (https://github.com/Rappsilber-

Laboratory/xiAnnotator).

xiSPEC itself consists of two major components: the data

handling back-end and the interactive data visualization

front-end. The backend data parser is written in python us-

ing the pymzML (20) (for mzML input) and pyteomics (21)

(for mzIdentML input) packages and is also available as an

open source project through GitHub (https://github.com/

Rappsilber-Laboratory/xiSPEC ms parser). For fast data

access into MGF files, xiSPEC uses an indexed based file

reader we derived from pymzML. The parsed data gets writ-

ten into a SQLite database. SQLite provides the benefit of

having a single separate file for each dataset. This enables

easy storage, deletion or compression of data. It is also

cross-platform stable. On an annotation request, the data

are read out from the database and converted into JSON.

The annotation of spectra is done on-demand via API com-

munication in JSON from the front-end to the Java appli-

cation xiAnnotator running on a separate server. The front-

Figure 1. Overview of xiSPEC workflow. The input for xiSPEC are peak

list data and peptide identifications. The user can either upload files di-

rectly to the xiSPEC server or select them from the PRIDE repository by

providing the PXD accession number. For single spectra analysis data can

be provided via HTML form input. Users can save datasets (publicly or

password protected) and share them using a unique URL. Results can be

exported as SVG for use in publications and presentations.

end is written in JavaScript. The spectra data-visualization

is based on D3 (22) to create SVGs. Event handling and

synchronization between different views is achieved using

the jQuery and Backbone JavaScript libraries. The inter-

active results tables are generated employing the DataTa-

bles jQuery library with server-side PHP processing for or-

dering, filtering and searching. This prevents processing of

large datasets leading to prolonged load times and browser

crashing.

FUNCTIONALITY

Data input

Users can provide data either by direct data upload of an

identifications and peak list file(s) pair or by providing a

PXD accession number to the PRIDE repository (23)and

subsequent selection of the files from the list of project

files (Figure 1). In the latter case, xiSPEC uses the PRIDE

RESTful API (24) to retrieve the project files. After user se-

lection the files are directly downloaded from the PRIDE

FTP server to the xiSPEC backend server where they are

processed. This relieves the user from downloading and

then re-uploading the files, thus making data deposited in

PRIDE accessible easier and independent of end-user in-

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Nucleic Acids Research, 2018, Vol. 46, Web Server issue W475

ternet connection speed. xiSPEC supports the PSI standard

proteomics identifications file format mzidentML and ad-

ditionally a simple csv file format for non-standard data.

This format is described at http://spectrumviewer.org/help.

php#csv (Supplementary Table S1). Supported peak list

data formats are the PSI standard mzML and also MGF.

xiSPEC supports compression archives in .gz and .zip for-

mats. For single spectra analysis users can input data di-

rectly via an HTML form with interactive peptide preview.

All three options are available through the Upload page of

the website.

Features

Opening a dataset in xiSPEC presents the user all avail-

able information on a single web page with inter-connected

views (Figure 2). Sub elements of the website layout can be

re-sized or hidden when they are not needed to accommo-

date different use cases and individual users’ preferences.

Datasets can be saved for later access or for sharing with

collaborators by using a unique URL. To save a dataset the

user has to input a name for his dataset and chose whether

it will be publicly available or private. If the user chooses

private the user needs to choose a password that will be re-

quired to access his dataset. In this way the dataset can still

be shared with collaborators or reviewers before making it

publicly available.

Identification results are presented to the user in an in-

teractive data table. Columns can be hidden to declutter the

view of unnecessary information. Results are paginated to

provide the user with the ability to view the results and plots

at the same time. The order of results can be changed sim-

ply by clicking on the column name. If more than one score

is present the user can select the score used for ordering via

a drop down menu. Results can be filtered by string search.

Additionally predefined filters are provided to toggle dis-

playing decoy identifications, identifications not passing the

threshold defined by the search software and to hide linear

identifications (useful for cross-link datasets). If the identifi-

cations input file contains alternative explanations they can

be easily accessed by switching to the ‘alternative explana-

tions’ tab. This allows for quick comparison and manual re-

viewing of potential misidentifications. The protein column

is automatically converted to a link to the UniProt (25) sub-

page for the corresponding protein if the accession number

is present in the input data.

The underlying data of the selected identification is pre-

sented to the user in multiple interactively connected views.

The two main ones being the annotated mass spectrum

(Figure 2A) with a peptide sequence fragmentation key

(Figure 2B). Matched fragment peaks (and their isotope

cluster peaks) are visualized through color and fragment

name labels. For cross-linking data, two different colors are

used to differentiate the two peptides. Neutral-loss frag-

ments are displayed in a lighter color. Additionally, spec-

tra quality control (QC) plots are generated to allow for

manual identification quality assessment. They show the er-

ror of matched fragments plotted over intensity (Figure 2C)

and over acquired m/zrange (Figure 2D). All of these views

are interactive SVG elements. Hovering over a data point in

any view displays a tooltip with detailed information. High-

lighting or selecting data points in any view is represented

in all other views so that the information available in the

different views can be leveraged together.

Detailed instructions to xiSPEC’s features can be

found on the help pages (http://spectrumviewer.org/help.

php#features). They are described as text instructions while

at the same time being displayed as GIFs to visually guide

the user. xiSPEC includes the following features:

(i) Zooming into spectra and moving around the cur-

rently displayed section. The current zoom level (m/z

range) can be locked, i.e. temporarily disabling the

zoom and move functionality in the current spectrum.

The selected m/zrange stays in place when switch-

ing spectra to enable easy cross-spectra comparison

of specific m/zregions.

(ii) Changing appearance styles of the output by chang-

ing color schemes and highlight color (Figure 3A).

(iii) Toggle display of neutral loss fragment labels, to de-

clutter the annotated spectrum.

(iv) Changing to absolute error values for the QC plots.

(v) Measuring distances between peaks in Thompson.

The distance is converted to masses calculated for

multiple charge states and possible amino acid

matches are displayed (Figure 3C). This can be help

analyzing unexplained peaks in the spectra.

(vi) Option to move labels for better visibility. This click

and drag functionality automatically creates dashed

lines to the corresponding peak which simplifies fig-

ure making (Figure 3C).

(vii) Adding new post-translational modifications (PSMs)

or changing modification masses. This can be done

through the data settings view, by typing non-

uppercase characters into the peptide sequence input

(Figure 3A). Modification masses can be changed in

the modification table. Inserting a modification that

is not present in the input data will result in adding a

row to the table.

(viii) Changing modification position. Modification posi-

tions can be moved from one residue to another by

first clicking on the modification in the peptide se-

quence fragmentation key view and then clicking on

the destination residue (Figure 3B). Alternatively, the

modification can be moved in the input sequence

(Figure 3A).

(ix) Changing cross-linker positions can be done by sim-

ply clicking on the cross-linker line in the peptide se-

quence fragmentation key view and selecting the new

destination residue (Figure 3D). Another way is to

move the cross-link symbol (#) in the input sequence

(Figure 3A). Specifications on the data input syntax

can be found in the help pages.

(x) Modifying precursor data, namely the precursor

charge state and the peptide sequence (amino acids

and modifications) (Figure 3A).

(xi) Changing fragment ion types considered. Ion types

currently supported are unfragmented precursor

(peptide) ion, b, c, y, z ions (Figure 3A).

(xii) Changing the permitted error tolerance for matching

fragment peaks (Figure 3A).

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W476 Nucleic Acids Research, 2018, Vol. 46, Web Server issue

Figure 2. SVG output of xiSPEC’s views for a cross-linked peptide example. (A) Peptide sequence with fragmentation key. Amino acid residues in one-

letter code. Lines show matched peptide fragments. Grayed-out residues are not included in currently selected fragment. (B) Annotated mass spectrum.

Matched peaks are colored and labeled (though labels of neutral-loss fragments are hidden in this example). (C) and (D) show spectra QC plots. Each

point represents a matched peak of the mass spectrum. (C) Fragment match error over peak intensity. (D) Match error over m/z. Coloring (red and blue)

is used to differentiate between the two peptides. Neutral-loss fragments are displayed in a lighter color. Yellow highlight is the currently selected fragment

(interconnected between all views).

Figure 3. xiSPEC feature examples. (A) Settings view. Peptide input data can be modified in the displayed tab. Appearance customization can be done

through the ‘appearance’ tab. (B) Changing PSM modification positions. (C) Use of measuring tool in zoomed-in excerpt of spectrum. Measure distance

between peaks with automatic calculation and amino-acid residue matching for multiple charge states. (D) Changing cross-linker position.

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Nucleic Acids Research, 2018, Vol. 46, Web Server issue W477

(xiii) Reverting back to original annotation after modify-

ing input data at the click of a button (background

color changes to visualize changed data).

Data output

xiSPEC offers the user the option to download single plots

in publication quality as easily modifiable vector graphics

(Figure 2). Additionally, xiSPEC allows sharing of visual-

ized datasets at the ease of just sharing an unique URL,

open or password protected. Anyone using a modern web

browser can access it without the need to install third party

software.

USE CASES

We imagine xiSPEC bringing a positive impact to individ-

uals from a variety of different backgrounds working with

mass spectrometry proteomics data. Users can be divided

into two main groups: (i) providers of data and (ii) users of

data.

Providers of data are for example staff of mass spectrom-

etry core facilities. They are not necessarily interested in in-

terpretation details, but have the obligation of communica-

tion, i.e. sharing the data with their users. Authors of pub-

lications that include mass spectrometry data also need a

way to make their annotated data available to their review-

ers and readers. In fact many proteomics field guidelines in-

clude making annotated mass spectra of published results

available (26–28), which can be achieved using xiSPEC by

either sharing the datasets unique URL or downloading

plots for use in publication. When still looking at data scien-

tists may benefit from the possibility of interactive sharing

with collaborators, other scientists or the community. An-

other example are teachers and lecturers who want to give

their students access to view and work with mass spectrom-

etry data. Removing the extra step of having to download

additional software lowers the entry barrier significantly.

Users of data, e.g. biologists who receive mass spectrom-

etry data from core facilities often have no dedicated soft-

ware installed. Installing and getting offline software to

work constitutes an additional hurdle, often involving frus-

tration from steep learning curves. We believe that xiSPEC

with its ease of use, user-centered and browser-based ap-

proach can simplify both lives of biologists and core facility

members. By providing intuitive and easy to use tools for

testing of hypothesis (measuring tool, re-annotation with

modified parameters and QC plots) we also see a benefit

for mass spectrometrists diving deeper into their data when

looking at non-standard results.

CONCLUSION

The importance of data sharing is widely appreciated in pro-

teomics and secured by initiatives like ProteomeXchange.

However, accessing, sharing and analyzing individual spec-

tra from proteomic datasets is very cumbersome. xiSPEC

aims to fill this gap by placing the user at the center of the in-

terface design offering multiple view synchronization and a

multitude of other features for hypothesis testing and shar-

ing. As an actively developed open-source tool, it is open to

community feature requests and contribution. We will be

working toward seamless integration with online reposito-

ries such as PRIDE, UniProt or INTACT for users to inter-

rogate primary data through simple web browsing.

DATA AVAILABILITY

xiSPEC is an open source collaborative initiative available

in the GitHub repositories (front-end: https://github.com/

Rappsilber-Laboratory/xiSPEC; back-end: https://github.

com/Rappsilber-Laboratory/xiSPEC ms parser). xiAnno-

tator is an open source collaborative initiative available

in the GitHub repository (https://github.com/Rappsilber-

Laboratory/xiAnnotator). All of which are freely available

under the Apache License v2.0.

SUPPLEMENTARY DATA

Supplementary Data are available at NAR Online.

ACKNOWLEDGEMENTS

We thank Jimi-Carlo Bukowski-Wills for creating xiSPEC

1.0 (accessible through http://legacy.spectrumviewer.org/;

source code available at http://sourceforge.net/projects/

spectrumviewer/), Lutz Fischer for creating the Java appli-

cation backend service for the annotation of spectra data

(https://github.com/Rappsilber-Laboratory/xiAnnotator)

and Martin Graham for his help with JavaScript libraries

and input on software design.

FUNDING

Einstein Foundation; Wellcome Trust Senior Research Fel-

lowship [103139 to J.R.]; Wellcome Trust Multi-user Equip-

ment Grant [108504]; Wellcome Centre for Cell Biology

[203149]. Funding for open access charge: Wellcome Cen-

tre for Cell Biology [203149].

Conflict of interest statement. None declared.

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