1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
|
<!DOCTYPE HTML PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xml:lang="cs" xmlns="http://www.w3.org/1999/xhtml" lang="cs"><head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<meta name="author" content="Created by Martin Strohalm PhD; www.biographics.cz">
<meta name="copyright" content="Martin Strohalm">
<meta name="keywords" content="mMass, mass spectrometry, open source, peaklist analysis, MALDI, martin strohalm, proteomics, bioinforatics" lang="en">
<meta name="description" content="Program mMass presents an open source package of simple tools for mass spectrometric data analysis. It consist of several modules and tools for protein sequence handling and mass spectrum interpretation with focus on common proteomic tasks." lang="en">
<title>mMass - Open Source MS Tool | Documentation | Introduction</title>
<link rel="icon" href="http://mmass.biographics.cz/favicon.ico" type="image/png">
<link rel="stylesheet" type="text/css" media="print" href="style_002.css">
<link rel="stylesheet" type="text/css" media="screen" href="style.css">
</head><body>
<div id="container">
<!-- page header -->
<div id="header">
<h1><a href="http://mmass.biographics.cz/" title="Homepage"><span>mMass - Open Source Mass Spectrometry Tool</span></a></h1>
<p id="jump"><a href="#mainMenu">Jump to main menu</a></p>
</div>
<!-- page content -->
<div id="content">
<!-- main panel -->
<div id="panelsMain">
<div id="documentation" class="panel">
<h2><span>Introduction</span></h2>
<p>Mass
spectrometry is involved in many fields of modern biochemistry. It has
become a common tool not only for precise mass measurement, but also
for protein identification, peptide sequencing, the identification of
various post-translational modifications, and even for the structural
characterization of proteins or protein complexes. A variety of
software tools exist for data analysis and interpretation, most of
which are specifically connected with individual instruments.</p>
<p>Because
mass spectrometry has primarily been used for large-scale protein
identification in recent years, most manufacturer software is focused
on this topic, together with the issue of automated high-throughput
analysis. Despite this, in many instances mass spectrometry experiments
still depend on the precise analysis of mass spectra, as well as on the
researcher's experience.</p>
<p>It is common practise for
commercial software tools to be tightly coupled to just one data
format. Such software can only be used to analyze data from a specific
instrument, and this causes serious problems for proteomic laboratories
that use more than one instrument. This tight software-instrument
relationship also causes problems for laboratories that do not possess
their own instruments, and have to obtain mass spectra from other,
collaborating, laboratories. Such laboratories have no opportunity to
check and/or re-analyze the raw data themselves.</p>
<p>To provide a solution to these problems we have developed <em>mMass</em>,
a package of many software tools for the precise analysis of mass
spectra with respect to common proteomic tasks. Following figure
illustrates the overall application schema. The first part of the
analysis process concerns simple user manipulation of the loaded
spectra, as well as peak labeling and data processing tasks, such as
(re)calibration. The second part enables a previously created peaklist
to be interpreted using one or more of the tools available, such as the
<a href="index.html/mcut.php" title="go to chapter">Protein Digest Tool</a>, <a href="index.html/mfrag.php" title="go to chapter">Peptide Fragmentation Tool</a>, <a href="index.html/mdiff.php" title="go to chapter">Check Differences Tool</a>, <a href="index.html/mcomp.php" title="go to chapter">Compare Peaklist Tool</a> and <a href="index.html/mmascot.php" title="go to chapter">Mascot Search Tools</a>.</p>
<div class="images">
<img src="figures/mmass_scheme.png" alt="mMass scheme">
<p>Overall scheme of mMass structure and workflow.</p>
</div>
</div>
<!-- main panel end -->
<hr id="mainStop">
</div>
<!-- side panels -->
<div id="panelsSide">
<div id="mainMenu" class="panel">
<h2><span>Main menu</span></h2>
<ul>
<li><a href="http://mmass.biographics.cz/" title="latest news"><span>News</span></a></li>
<li><a href="features.html" title="mMass main features"><span>Features</span></a></li>
<li><a href="http://mmass.biographics.cz/en/download.php" title="download source files or binary distribution"><span>Download</span></a></li>
<li><a href="index.html" title="detailed mMass description"><span>Documentation</span></a></li>
<li><a href="http://mmass.biographics.cz/en/message.php" title="send bug report, function request etc."><span>Contact</span></a></li>
</ul>
</div>
<div id="chapters" class="panel">
<h2><span>Chapters</span></h2>
<ul>
<li><a href="index.html" title="mMass structure..."><span>Introduction</span></a></li>
<li><a href="mmass.html" title="Layout, menubar, toolbar, statusbar..."><span>Application layout</span></a></li>
<li><a href="mdoc.html" title="Open, save, print, export, info..."><span>Document basics</span></a></li>
<li><a href="mspec.html" title="Spectrum manipulations, peaks labelling, comparison..."><span>Spectrum viewer</span></a></li>
<li><a href="mpeak.html" title="Peaklist options..."><span>Peaklist panel</span></a></li>
<li><a href="mproc.html" title="Calibration, crop..."><span>Data processing</span></a></li>
<li><a href="mseq.html" title="Sequence editting, modifications, search for mass..."><span>Sequence editor</span></a></li>
<li><a href="mcut.html" title="In silicio protein digest..."><span>Protein digest</span></a></li>
<li><a href="mfrag.html" title="In silicio peptide fragmentation..."><span>Peptide fragmentation</span></a></li>
<li><a href="mdiff.html" title="Check differences among all the peaks in peaklist..."><span>Check differences</span></a></li>
<li><a href="mcomp.html" title="Compare multiple peaklists..."><span>Compare peaklists</span></a></li>
<li><a href="mmatch.html" title="Match teoretical data to spectrum..."><span>Data matching</span></a></li>
<li><a href="mmascot.html" title="Mascot search tools..."><span>Mascot tools</span></a></li>
</ul>
</div>
<!-- side panels end -->
</div>
<!-- overflow block -->
<div id="contentStop"></div>
<!-- page content end -->
</div>
<!-- page footer -->
<div id="footer">
<p>© Martin Strohalm</p>
</div>
<!-- container end -->
</div>
</body></html>
|
