- 04
+
- FAIR & AI-ready data
FAIR data principles
-Public proteomics data only becomes scientifically reusable when it is described in a way that both people and machines can understand. We therefore work on metadata annotation, data standards, and community-facing tools that make proteomics data findable, accessible, interoperable, and reusable. Resources such as lesSDRF and annotation workflows around public repositories help turn deposited datasets into structured research objects that can be searched, compared, reprocessed, and used for machine learning. We want to move proteomics from data availability to data usability, where public datasets can support new questions beyond the study for which they were originally generated.
+Public proteomics data only becomes reusable, by people or by machines, when it is well described. We work on metadata annotation, data standards, and community tools that make proteomics data findable, accessible, interoperable, and reusable, and increasingly, ready to train AI models directly. This is a community effort rather than something we do alone. Through PSI-AI we help shape metadata standards for AI use. ProteomicsML gives us a place to curate machine-learning-ready benchmark datasets and teach others how to apply AI to proteomics, and projects such as mzPeak and rusteomics give us fast, open tooling that makes parsing and reusing mass spectrometry data less painful. Resources such as lesSDRF and annotation workflows around public repositories turn deposited datasets into structured objects that can be searched, compared, reprocessed, and used to train models. The underlying goal is to move proteomics data from merely available to actually usable, for new scientific questions and new AI models, beyond the study that originally produced it.
- 05
+
- Reprocessing
Reprocessing
-Reprocessing brings our research lines together: peptide-property prediction improves how we model analyte behaviour, identification and rescoring software recover confident evidence from complex spectra, and FAIR annotation makes public datasets comparable at scale. We combine these developments to revisit existing proteomics data with new computational questions, extracting biological information that was not accessible in the original analysis. This includes large-scale tissue profiling, biomarker discovery, and the systematic recovery of previously missed post-translational modifications, as illustrated by Scop3PTM. Our aim is to make public proteomics data scientifically active beyond deposition, turning the vast amount of data that already exists into a continuing source of new biological insight.
+Reprocessing pulls our other research lines together. Peptide-property prediction improves how we model analyte behaviour, identification and rescoring software recovers confident evidence from complex spectra, and FAIR/AI-ready annotation makes public datasets comparable at scale. We use these pieces together to revisit existing proteomics data with new computational questions and pull out biological information the original analysis did not capture. Recent examples include large-scale tissue profiling, biomarker discovery, and the systematic recovery of post-translational modifications that were missed the first time, as in Scop3PTM. The aim is to keep public proteomics data scientifically active after deposition, so that data already collected can keep producing new findings, not just the ones from its original study.
+ Ben Binke
+
+
Alumni & Former Colleagues
diff --git a/team/teams.scss b/team/teams.scss index e3a1a01..ec56d36 100644 --- a/team/teams.scss +++ b/team/teams.scss @@ -2,12 +2,298 @@ #title-block-header { display: none !important; } +// ── Team grid + cards + profile expander ───────────────────────────────────── +// All team-page card styling lives here (moved out of assets/compomics.scss) so +// the two stylesheets can't fight over the same selectors. .team-grid { + display: grid; + grid-template-columns: repeat(auto-fill, minmax(150px, 1fr)); + gap: 2.2rem 1.4rem; + margin: 2.5rem 0; + @media (min-width: 860px) { grid-template-columns: repeat(5, 1fr); } } +.team-card-wrap { display: contents; } + +.team-grid-selectors { margin-bottom: 1.75rem; } + +.team-card { + display: flex; + flex-direction: column; + align-items: center; + text-align: center; + text-decoration: none; + color: inherit; + transition: transform 0.18s ease; + + appearance: none; + border: none; + background: transparent; + padding: 0; + cursor: pointer; + + &:hover { + transform: translateY(-5px); + text-decoration: none; + color: inherit; + + .team-photo { + filter: grayscale(0%); + border-color: $primary; + box-shadow: 0 8px 24px rgba(0, 0, 0, 0.18), 0 0 0 3px rgba(31, 95, 143, 0.12); + } + .team-name { color: $primary; } + } + + &.is-selected { + .team-photo { + filter: grayscale(0%); + border-color: $primary; + box-shadow: 0 0 0 4px rgba(31, 95, 143, 0.08); + } + .team-name { color: $primary; } + } +} + +.team-photo { + width: 150px; + height: 150px; + border-radius: 50%; + object-fit: cover; + object-position: center top; + border: 1px solid $line; + box-shadow: none; + margin-bottom: 0.75rem; + display: block; + transition: filter 0.2s ease, box-shadow 0.2s ease, border-color 0.2s ease; + filter: grayscale(12%); + + &:hover { filter: grayscale(0%); } +} + +.team-name { + font-family: $font-family-heading; + font-size: 1.02rem; + font-weight: 700; + color: $ink; + margin-bottom: 0.1rem; + line-height: 1.3; + height: calc(1.02rem * 1.3 * 2); + display: flex; + align-items: center; + justify-content: center; +} + +.team-role { + font-family: $font-family-sans-serif; + font-size: 0.74rem; + text-transform: uppercase; + letter-spacing: 0.06em; + color: $muted; + line-height: 1.35; +} + +.team-section-title { + font-family: $font-family-sans-serif; + font-size: 0.78rem; + font-weight: 700; + text-transform: uppercase; + letter-spacing: 0.1em; + color: $muted; + margin: 3rem 0 0.5rem; + padding-bottom: 0.5rem; + border-bottom: 1px solid $line; +} + +.team-shell-intro { + max-width: none; + margin-bottom: 1rem; + + p { + margin: 0.35rem 0 0; + color: $muted; + font-size: 0.94rem; + line-height: 1.7; + } +} + +// Shared dark panel look +.team-detail-panel, +.team-profile-expander { + position: relative; + margin-top: 2rem; + padding: clamp(1.6rem, 3.5vw, 2.8rem); + border-radius: 1rem; + overflow: hidden; + border: 1px solid rgba(90, 167, 218, 0.20); + background: linear-gradient(135deg, #0d1f38, #142d50); + box-shadow: 0 24px 70px rgba(0, 0, 0, 0.32), 0 0 0 1px rgba(90, 167, 218, 0.08); + + &[hidden] { display: none; } + + &::before { + content: ""; + position: absolute; + inset: 0; + background: + radial-gradient(circle at top right, rgba(90, 167, 218, 0.22), rgba(90, 167, 218, 0) 42%), + linear-gradient(135deg, rgba(10, 20, 40, 0.20), rgba(10, 20, 40, 0.55)); + pointer-events: none; + } +} + +// The expander spans the whole row so its width is identical for every member +// and the pointer notch can sit under any card in the row. Content fills the +// full width (justified) so there is no empty band of background on the right. +.team-profile-expander { + grid-column: 1 / -1; + margin-top: 0.5rem; + margin-bottom: 1rem; + display: grid; + gap: 1.15rem; + color: #f6f2ea; + + max-height: 0; + opacity: 0; + transition: max-height 0.45s cubic-bezier(0.4, 0, 0.2, 1), opacity 0.3s ease; + + &::after { + content: ""; + position: absolute; + top: -8px; + left: var(--notch-x, 50%); + transform: translateX(-50%); + width: 0; + height: 0; + border-left: 8px solid transparent; + border-right: 8px solid transparent; + border-bottom: 8px solid #0d1f38; + pointer-events: none; + z-index: 2; + } +} + +.team-detail-copy { + position: relative; + z-index: 1; + display: grid; + gap: 1.15rem; + color: #f6f2ea; +} + +.team-detail-header { + display: grid; + gap: 0.35rem; +} + +.team-detail-eyebrow { + font-family: $font-family-sans-serif; + font-size: 0.72rem; + font-weight: 700; + letter-spacing: 0.14em; + text-transform: uppercase; + color: rgba(255, 255, 255, 0.72); +} + +.team-detail-header h3 { + margin: 0; + font-size: clamp(2rem, 4vw, 2.8rem); + color: #fff; + line-height: 1.08; +} + +.team-detail-role { + margin: 0; + color: rgba(255, 255, 255, 0.8); + font-size: 0.92rem; + letter-spacing: 0.03em; +} + +.team-detail-section { + padding-top: 0.35rem; + + h4 { + margin: 0 0 0.35rem; + color: rgba(255, 255, 255, 0.88); + font-family: $font-family-heading; + font-size: 0.9rem; + text-transform: none; + letter-spacing: -0.01em; + } + + p { + margin: 0; + color: rgba(255, 255, 255, 0.9); + line-height: 1.8; + font-size: 0.98rem; + text-align: justify; + hyphens: auto; + } +} + +.team-pub-list { + display: flex; + flex-direction: column; + gap: 0.45rem; +} + +.team-pub-item { + display: flex; + flex-wrap: wrap; + align-items: baseline; + gap: 0.25rem 0.6rem; + padding: 0.45rem 0.8rem; + border: 1px solid rgba(90, 167, 218, 0.28); + border-radius: 0.4rem; + background: rgba(255, 255, 255, 0.04); + text-decoration: none; + cursor: pointer; + transition: border-color 0.15s ease, background 0.15s ease, box-shadow 0.15s ease; + + &::after { + content: "↗"; + font-size: 0.7rem; + color: rgba(90, 167, 218, 0.55); + align-self: center; + margin-left: auto; // push the arrow to the right edge of the full-width row + transition: color 0.15s ease, transform 0.15s ease; + display: inline-block; + } + + &:hover { + border-color: rgba(90, 167, 218, 0.65); + background: rgba(90, 167, 218, 0.12); + box-shadow: 0 0 12px rgba(90, 167, 218, 0.18); + text-decoration: none; + + &::after { + color: rgba(90, 167, 218, 0.95); + transform: translate(1px, -1px); + } + } +} + +.team-pub-title { + font-family: $font-family-heading; + font-size: 0.88rem; + font-weight: 600; + color: rgba(255, 255, 255, 0.95); + line-height: 1.3; +} + +.team-pub-venue { + font-family: $font-family-sans-serif; + font-size: 0.72rem; + font-weight: 600; + text-transform: uppercase; + letter-spacing: 0.08em; + color: rgba(90, 167, 218, 0.85); + white-space: nowrap; +} + .page-hero-band { position: relative; left: 50%; @@ -36,9 +322,10 @@ background: linear-gradient(to bottom, rgba(6,8,12,.55) 0%, - rgba(6,8,12,.22) 55%, + rgba(6,8,12,.22) 30%, + rgba(6,8,12,.34) 65%, var(--bs-body-bg) 100%), - linear-gradient(135deg, rgba(31,95,143,.18), rgba(0,0,0,0) 60%); + linear-gradient(135deg, rgba(31,95,143,.18), rgba(0,0,0,0) 80%); } @@ -49,7 +336,8 @@ display: flex; flex-direction: column; justify-content: flex-end; - padding: 0 1.5rem clamp(1.8rem, 4.5vh, 3rem); + padding: 0 2.5rem clamp(1.8rem, 4.5vh, 3rem); + justify-content: center; } .page-hero-kicker { diff --git a/tools/index.qmd b/tools/index.qmd index fc0464d..599012e 100644 --- a/tools/index.qmd +++ b/tools/index.qmd @@ -93,6 +93,33 @@ toc: false }, devs: ['robbin', 'ralf'] }, + { + name: 'iDeepLC', cat: 'prediction', icon: 'bi-clock-history', logo: 'ideeplc.png', + desc: 'Retention-time prediction from peptide chemical structure (SMILES), generalising to modifications unseen during training.', + links: { + github: 'https://github.com/compomics/iDeepLC', + paper: 'https://doi.org/10.1021/acs.analchem.5c08017', + }, + devs: ['alireza', 'robbin'] + }, + { + name: 'CALLC', cat: 'prediction', icon: 'bi-clock-history', logo: 'callc.png', + desc: 'Generalized calibration that maps retention-time predictions between different liquid chromatography setups, avoiding setup-specific models.', + links: { + github: 'https://github.com/CompOmics/CALLC', + paper: 'https://doi.org/10.1021/acs.analchem.0c00233', + }, + devs: ['robbin'] + }, + { + name: 'peptide-GNN', cat: 'prediction', icon: 'bi-diagram-3', comingSoon: true, + desc: 'Graph neural network for interpretable peptide retention-time prediction.', + links: { + github: 'https://github.com/CompOmics/peptide-gnn', + paper: 'https://doi.org/10.64898/2026.05.18.725893', + }, + devs: ['robbin', 'alex'] + }, { name: 'IM2Deep', cat: 'prediction', icon: 'bi-wind', logo: 'im2deep.svg', desc: 'Predicts collisional cross-section (CCS) values for peptides, including modified, and multiple conformations.', @@ -194,6 +221,7 @@ toc: false desc: 'Comprehensive resource of human phosphosites mapped within their full structural context.', links: { github: 'https://github.com/compomics', + web: 'https://iomics.ugent.be/scop3p/', paper: 'https://doi.org/10.1021/acs.jproteome.0c00306', }, devs: ['pathmanaban', 'natalia'] @@ -201,7 +229,10 @@ toc: false { name: 'Scop3PTM', cat: 'biological', icon: 'bi-diagram-3-fill', logo: 'scop3ptm.png', desc: 'Maps post-translational modifications onto protein structures for contextual, structure-aware analysis.', - links: { github: 'https://github.com/compomics' }, + links: { + github: 'https://github.com/compomics', + web: 'https://iomics.ugent.be/scop3ptm', + }, devs: ['pathmanaban', 'natalia'] }, { @@ -209,6 +240,7 @@ toc: false desc: 'Machine-learning framework for tissue inference and biomarker discovery from proteomes.', links: { github: 'https://github.com/compomics', + web: 'https://mlmarker.streamlit.app/', paper: 'https://doi.org/10.1101/2025.06.10.658642', }, devs: ['tine'] @@ -219,9 +251,18 @@ toc: false links: { github: 'https://github.com/compomics' }, devs: ['enrico'] }, + { + name: 'PTMVision', cat: 'biological', icon: 'bi-eye', logo: 'ptmvision.png', + desc: 'Interactive web platform for exploratory visual analysis of post-translational modifications from mass spectrometry data.', + links: { + web: 'https://ptmvision-tuevis.cs.uni-tuebingen.de/', + paper: 'https://doi.org/10.1021/acs.jproteome.4c00679', + }, + devs: ['caro'] + }, { name: 'E. coli PeptideAtlas Build', cat: 'biological', icon: 'bi-virus', logo: 'bacterium.png', - desc:'Characterizing the observed Eschericia coli pan-proteome and its post-translational modifications.', + desc:'Characterizing the observed Escherichia coli pan-proteome and its post-translational modifications.', links: { web: 'https://peptideatlas.org/builds/ecoli/', paper: 'https://doi.org/10.1021/acs.jproteome.5c00902' @@ -292,6 +333,15 @@ toc: false paper: 'https://doi.org/10.1021/acs.jproteome.5c00435', }, devs: ['tim','ralf'] + }, + { + name: 'PSI-AI', cat: 'community', icon: 'bi-filetype-ai', + desc: 'Working group making proteomics data AI-ready and standardizing the use of AI in data analysis workflows.', + note: 'A HUPO-PSI community initiative.', + links: { + web: 'https://psi-ai.org/', + }, + devs: ['ralf', 'tine', 'hari'] } ]; @@ -370,12 +420,15 @@ toc: false } html += '';
- // devs (own row, above the links)
+ // devs (own row, above the links) — each avatar links to that person's team entry
if (tool.devs && tool.devs.length) {
- html += '
';
+ html += '
';
tool.devs.slice(0, 4).forEach(function (key) {
- html += ' + '.jpg)
';
+ const devName = key.charAt(0).toUpperCase() + key.slice(1);
+ html += ''
+ + ''
+ + '';
});
html += '
';
}
diff --git a/tools/tools.scss b/tools/tools.scss
index 608dfb8..9a5fb38 100644
--- a/tools/tools.scss
+++ b/tools/tools.scss
@@ -362,7 +362,29 @@ $cat-community: #4f9d6b; // green (community projects)
align-self: flex-start; // avatars hug the left, don't stretch
}
+.tool-tile-dev-link {
+ display: block;
+ line-height: 0;
+ border-radius: 50%;
+ transition: transform 0.15s ease;
+
+ &:not(:first-child) { margin-left: -8px; }
+
+ // lift above overlapping siblings on hover/focus so the whole avatar is visible
+ &:hover,
+ &:focus-visible {
+ transform: translateY(-3px);
+ z-index: 1;
+ }
+
+ &:focus-visible {
+ outline: 2px solid $primary;
+ outline-offset: 2px;
+ }
+}
+
.tool-tile-dev {
+ display: block;
width: 26px;
height: 26px;
border-radius: 50%;
@@ -371,8 +393,6 @@ $cat-community: #4f9d6b; // green (community projects)
border: 2px solid $cream-2;
background: $cream-3;
- &:not(:first-child) { margin-left: -8px; }
-
.tool-tile:hover & { border-color: $surface-hover; }
}
diff --git a/tutorials/posts/2026-06-01-bioinformatics-for-proteomics.qmd b/tutorials/posts/2026-06-01-bioinformatics-for-proteomics.qmd
new file mode 100644
index 0000000..937b33b
--- /dev/null
+++ b/tutorials/posts/2026-06-01-bioinformatics-for-proteomics.qmd
@@ -0,0 +1,260 @@
+---
+title: "Bioinformatics for Proteomics"
+date: 2026-06-01
+description: "The original hands-on CompOmics course on mass spectrometry-based proteomics data analysis: identification, functional analysis, data sharing, and quantification. Slides and exercise resources included. A modernised version is in preparation."
+categories: [proteomics, course, identification, quantification, data-sharing, searchgui, peptideshaker]
+---
+
+```{=html}
+';
+ const devName = key.charAt(0).toUpperCase() + key.slice(1);
+ html += ''
+ + ''
+ + '';
});
html += '
+
+
+
+ 1
+
+
+
+
+
+
+ 2
+
+
+
+
+
+
+ 3
+
+
+
+
+
+
+ 4
+
+
+
+
+```
diff --git a/tutorials/tutorials.scss b/tutorials/tutorials.scss
index 731bdc7..670ebe6 100644
--- a/tutorials/tutorials.scss
+++ b/tutorials/tutorials.scss
@@ -41,3 +41,217 @@
max-width: 62ch;
margin: 0;
}
+
+// ── "Bioinformatics for Proteomics" course page ──────────────────────────────
+// A numbered lab-manual layout: each module is a chapter, each step hangs off a
+// left rail (the workflow is a real sequence, so the numbering carries meaning).
+// Resources are type-coded chips — blue for materials, red for external tools.
+// Scoped under .bfp so nothing leaks to other posts.
+.bfp {
+ --bfp-rail: 3rem; // width of the number column
+ --bfp-gap: 1.4rem; // rail-to-content gap
+ max-width: 46rem;
+
+ .bfp-lead {
+ font-family: $font-family-sans-serif;
+ font-size: 1.16rem;
+ line-height: 1.6;
+ color: $ink;
+ max-width: 40rem;
+ margin: 0.25rem 0 1.6rem;
+ }
+
+ // ── Notes (archived banner + inline deprecation) ──────────────────────────
+ .bfp-note {
+ display: flex;
+ gap: 0.8rem;
+ padding: 0.9rem 1.1rem;
+ background: $cream-2;
+ border: 1px solid $line;
+ border-left: 3px solid $primary;
+ border-radius: 0 0.4rem 0.4rem 0;
+ margin: 1.5rem 0;
+
+ > i {
+ flex-shrink: 0;
+ color: $primary;
+ font-size: 1.15rem;
+ margin-top: 0.1rem;
+ }
+
+ p {
+ margin: 0;
+ font-family: $font-family-sans-serif;
+ font-size: 0.93rem;
+ line-height: 1.6;
+ color: $ink-soft;
+ }
+ p + p { margin-top: 0.4rem; }
+ strong { color: $ink; font-weight: 700; }
+
+ .bfp-note-meta { color: $muted; font-size: 0.85rem; }
+ }
+
+ .bfp-note--inline {
+ border-left-color: $secondary;
+ margin: 0 0 1.5rem;
+ > i { color: $secondary; }
+ }
+
+ // ── Course-wide / related resource rows ───────────────────────────────────
+ .bfp-general { margin: 1.5rem 0 2rem; }
+ .bfp-related { margin-top: 1.3rem; padding-left: calc(var(--bfp-rail) + var(--bfp-gap)); }
+ .bfp-loose { padding-left: calc(var(--bfp-rail) + var(--bfp-gap)); }
+
+ .bfp-general-label,
+ .bfp-related-label {
+ display: block;
+ font-family: $font-family-monospace;
+ font-size: 0.68rem;
+ font-weight: 700;
+ text-transform: uppercase;
+ letter-spacing: 0.16em;
+ color: $muted;
+ margin-bottom: 0.55rem;
+ }
+
+ // ── Module (chapter) ──────────────────────────────────────────────────────
+ .bfp-module { margin-top: 3.2rem; }
+
+ .bfp-module-head {
+ display: grid;
+ grid-template-columns: var(--bfp-rail) 1fr;
+ column-gap: var(--bfp-gap);
+ align-items: start;
+ margin-bottom: 1.3rem;
+ }
+
+ .bfp-module-num {
+ font-family: $font-family-heading;
+ font-weight: 800;
+ font-size: 2.3rem;
+ line-height: 1;
+ color: $primary;
+ text-align: right;
+ letter-spacing: -0.02em;
+ }
+
+ .bfp-eyebrow {
+ display: block;
+ font-family: $font-family-monospace;
+ font-size: 0.68rem;
+ font-weight: 700;
+ text-transform: uppercase;
+ letter-spacing: 0.16em;
+ color: $muted;
+ margin-bottom: 0.25rem;
+ }
+
+ .bfp-module-title {
+ font-family: $font-family-heading;
+ font-size: 1.7rem;
+ font-weight: 800;
+ color: $ink;
+ line-height: 1.1;
+ margin: 0 0 0.4rem;
+ padding: 0;
+ border: none;
+ }
+
+ .bfp-module-desc {
+ font-family: $font-family-sans-serif;
+ font-size: 0.96rem;
+ line-height: 1.6;
+ color: $ink-soft;
+ margin: 0;
+ max-width: 38rem;
+ }
+
+ // ── Steps hanging off the rail ────────────────────────────────────────────
+ .bfp-steps {
+ list-style: none;
+ margin: 0;
+ padding: 0;
+ }
+
+ .bfp-step {
+ display: grid;
+ grid-template-columns: var(--bfp-rail) 1fr;
+ column-gap: var(--bfp-gap);
+ }
+
+ .bfp-step-num {
+ font-family: $font-family-monospace;
+ font-size: 0.9rem;
+ font-weight: 700;
+ color: $primary;
+ text-align: right;
+ padding-top: 0.15rem;
+ }
+
+ .bfp-step-body {
+ border-left: 2px solid darken($line, 22%); // stacked borders form the continuous rail
+ padding: 0 0 1.35rem var(--bfp-gap);
+ }
+ .bfp-step:last-child .bfp-step-body { padding-bottom: 0.35rem; }
+
+ .bfp-step-title {
+ font-family: $font-family-heading;
+ font-size: 1.04rem;
+ font-weight: 700;
+ color: $ink;
+ line-height: 1.25;
+ margin: 0 0 0.5rem;
+ padding: 0;
+ border: none;
+ }
+
+ // ── Resource chips ────────────────────────────────────────────────────────
+ .bfp-links {
+ display: flex;
+ flex-wrap: wrap;
+ gap: 0.4rem;
+ }
+
+ .bfp-link {
+ display: inline-flex;
+ align-items: center;
+ gap: 0.4rem;
+ padding: 0.3rem 0.7rem;
+ font-family: $font-family-sans-serif;
+ font-size: 0.8rem;
+ font-weight: 600;
+ line-height: 1;
+ color: $ink-soft;
+ background: $cream-2;
+ border: 1px solid $line;
+ border-radius: 0.4rem;
+ text-decoration: none;
+ transition: border-color 0.15s ease, color 0.15s ease, background 0.15s ease;
+
+ i { font-size: 0.9rem; color: $primary; }
+
+ &:hover {
+ border-color: $primary;
+ color: $primary;
+ background: $surface-hover;
+ text-decoration: none;
+ }
+ }
+
+ // external software gets the red accent, so tools read differently from materials
+ .bfp-link--tool {
+ i { color: $secondary; }
+ &:hover { border-color: $secondary; color: $secondary; }
+ }
+
+ // ── Narrow screens: shrink the rail, keep the spine ───────────────────────
+ @media (max-width: 560px) {
+ --bfp-rail: 2.2rem;
+ --bfp-gap: 0.9rem;
+
+ .bfp-module-num { font-size: 1.9rem; }
+ .bfp-module-title { font-size: 1.45rem; }
+ .bfp-step-num { font-size: 0.82rem; }
+ }
+}
The classic Bioinformatics for Proteomics course: a hands-on walk through a full mass spectrometry data-analysis pipeline, from a raw spectrum file to a shared, quantified result. Work through the four modules in order, or jump to the step you need.
+ +
+
+
+
+
+
+ Archived materials. This page preserves the original course. Some tools, formats, and versions reflect the field as it was when the course was written and are now partly outdated (for example, PRIDE XML has been superseded by mzIdentML and mzTab). A modernised version is in preparation.
+ +
+ Course-wide
+
+
+
+
+
+ Module
+
+ Identification
+The full path from a raw file to validated peptides and proteins: format conversion, spectrum processing, database preparation, peptide-spectrum matching, inference, validation, PTM analysis, and de novo sequencing.
+-
+
-
+ 1.1
+ ++
Database generation
++ Course notes ++
+ -
+ 1.2
+ ++
Peak list generation
+ +
+ -
+ 1.3
+ ++
Peptide to spectrum matching
+ +
+ -
+ 1.4
+ ++
Browsing identification results
+ +
+ -
+ 1.5
+ ++
Peptide and protein validation
++ Course notes + PeptideShaker ++
+ -
+ 1.6
+ ++
PTM analysis
+ +
+ -
+ 1.7
+ ++
De novo peptide identification
+ +
+
+ Module
+
+ Functional analysis
+Turning an identification list into biology: retrieving protein information, pathway analysis, 3D structure visualisation, and Gene Ontology annotation.
+
+
+
+ Course notes
+ Exercise data
+
+
+ Module
+
+ Data sharing
+Submitting and reusing data through community repositories: converting results to standard formats, submitting to PRIDE and ProteomeXchange, browsing published datasets, and reprocessing.
+
+
+
+
+ -
+
-
+ 3.0
+ ++
Introduction
++ Course notes ++
+ -
+ 3.1
+ ++
Submit
++ Course notes + Exercise data ++
+ -
+ 3.2
+ ++
Browse
++ Course notes + Exercise data ++
+ -
+ 3.3
+ ++
Reprocess
++ Course notes ++
+
+ Module
+
+ Quantification
+Estimating protein abundance across several orders of magnitude, covering the main quantification strategies and their trade-offs.
+-
+
-
+ 4.0
+ ++
Introduction
++ Course notes ++
+ -
+ 4.1
+ ++
Spectrum counting
++ Course notes + PeptideShaker ++
+ -
+ 4.2
+ ++
Reporter ions
+ +
+ -
+ 4.5
+ ++
Statistical analysis
+ +
+