NOT all about proteomics — in deepth wiki about proteomics

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1/200 of the biomass threshold
A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards
A comparison between the sulfhydryl reductants tris(2-carboxyethyl)phosphine and dithiothreitol for use in protein biochemistry
A comprehensive review on Optimal conditions for carrying out trypsin digestions on complex proteomes
A new view of the tree of life
A Proteomics Approach to the Protein Normalization Problem: Selection of Unvarying Proteins for MS-Based Proteomics and Western Blotting
A Simple Elution Strategy for Biotinylated Proteins Bound to Streptavidin Conjugated Beads using Excess Biotin and Heat
A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies
About Perseus
Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides
Accurate multiplexed proteomics at the MS2 level using the complement reporter ion cluster
Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ
Accurate, Sensitive, and Precise Multiplexed Proteomics Using the Complement Reporter Ion Cluster
Acquisition and Analysis of DIA-Based Proteomic Data: A Comprehensive Survey in 2023
Advancement in protein inference from shotgun proteomics using peptide detectability
Advances in the clinical use of metaproteomics
AFA: Adaptive Focused Acoustics
AI learning tools
Alessandro Tanca
all ion fragmentation
Amazing performance on Astral
AMR database
An old method facing a new challenge: re-visiting housekeeping proteins as internal reference control for neuroscience research
Anaerostipes hadrus
Antimicrobial peptides (AMPs)
Assessing species biomass contributions in microbial communities via metaproteomics
Astral Applications
Astral MS
Automated sample preparation with SP3 for low‐input clinical proteomics
AVrC： Aggregated Gut Viral Catalogue
backlink footer template
Bacterial Cell sorting on flow cytometry
bacterial species
Benjamin Orsburn
Beyond protein lists: AI-assisted interpretation of proteomic investigations in the context of evolving scientific knowledge
Bias in False Discovery Rate Estimation in Mass-Spectrometry-Based Peptide IdentificationClic
Big Names
Bing Zhang
BioID
Bioinformatic tools for Metaproteomics
biomass difference
Bookmarks
Brian C. Searle
CamelCase Links
Candida albicans
Cazy
CAZymes
CDF normalization
CGR2: The genomic landscape of reference genomes of cultivated human gut bacteria
Challenging the Astral mass analyzer to quantify up to 5,300 proteins per single cell at unseen accuracy to uncover cellular heterogeneity
Christina Ludwig
Cladogram
CNN explainer
COG
color code in maxquant output
column dimension and peak width
Column Regeneration
combine peptide probability to protein level
Community ecology as a framework for human microbiome research
composition of dry human feces
compositional data
Consistency with the concept of nestedness
Constructing a dietary protein database
cool app
Core facilities
core facilities in uottawa
correlation analysis
Correlation: Pearson VS Spearman
CRAN Task Views
Cursor rules
Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota
Data-Independent Acquisition Mass Spectrometry in Metaproteomics of Gut Microbiota—Implementation and Computational Analysis
Data-independent acquisition: A milestone and prospect in clinical mass spectrometry-based proteomics
database for human gut metaproteomics
David Gómez-Varela
David L. Tabb
dbCAN-seq
DBCGR2
DBReducer
DDIA
DDM
De Novo from DIA
Dear-DIAXMBD: Deep Autoencoder Enables Deconvolution of Data-Independent Acquisition Proteomics
Deciphering functional redundancy in the human microbiome
Decoy database searches are problematic for large database
Deep learning
DeepDetect
DeepDIA
DIA analysis tool
DIA for metaproteomics
DIA for tongue coating for gastric cancer
DIA history
DIA metaproteomics on Astral
DIA on gut microbiome from colorectal cancer
DIA pushes proteomics from spectrum centric to peptide centric
DIA VS TMT
DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput
DIA-Umpire
Diann key parameters
diann result and filtering
DIANN's more technical details
Digestion after BioID
directDIA
directLFQ
DirectMS1: MS/MS-Free Identification of 1000 Proteins of Cellular Proteomes in 5 Minutes
dissociation constant
Diversity
DMSO enchance Microflow through Postcolumn Addition
DMSO enchances ESI
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Draft of 'Hyungwon Choi' by Beshy
Draft of 'New Tiddler' by Beshy
Draft of 'Posterior error probabilities and false discovery rates: two sides of the same coin' by Beshy
Dynamic Data Independent Acquisition
EASI-tag enables accurate multiplexed and interference-free MS2-based proteome quantification
EasyPhos in 2018
Efficient generation of open multi-stage fragmentation mass spectral libraries
Emma Allen-Vercoe
EncyclopeDIA
epoch, iteration, batch size
ESI commercials
Estimating relative biomasses of organisms in microbiota using phylopeptidomics
Estimating the confidence of peptide identifications without decoy databases
Evaluating False Transfer Rates from the Match-between-Runs Algorithm with a Two-Proteome Model
Evaluation of FASP, SP3, and iST Protocols for Proteomic Sample Preparation in the Low Microgram Range
Extensive DIA method comparison
False Discovery Rates and Related Statistical Concepts in Mass Spectrometry-Based Proteomics
fast DIA outperforms TMT for metaproteomics
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FDR accumulation in proteomics
Fight: why we need metaproteomics?
Fisher's 精确检验
fractionation on Astral DIA
Frequent used online tools
frequently used
Fully Automated Workflow for Integrated Sample Digestion and Evotip Loading Enabling High-Throughput Clinical Proteomics
Function is what counts
functional redundancy
Functional Redundancy Instead of Species Redundancy Determines Community Stability in a Typical Steppe of Inner Mongolia
Fusobacterium nucleatum
gene content network
Generating image by AI
genome size
glaDIAtor
Global compositional and functional states of the human gut microbiome in health and disease
glycan utilization loci
GNPS
Good dataset
Good Figures
GSEA analysis
GSVA
Guild and Niche Determination Enable Targeted Alteration of the Microbiome
Guild and niche in microbiome
Guild-based analysis for understanding gut microbiome in human health and diseases
Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes
Gut microbiota composition correlates with diet and health in the elderly
gut virome
H2O AutoML
Hamilton liquid handler learning
HDF5
Heather Armstrong
High-throughput proteomic sample preparation using pressure cycling technology
HILIC
Hill Numbers
Housekeeping proteins: a preliminary study illustrating some limitations as useful references in protein expression studies
how many missing values are there in DDA/DIA
How to speed up the tryptic digestion?
How to talk about protein‐level false discovery rates in shotgun proteomics
Hugging Face
hugging face chat
Hybrid-DIA
Hyungwon Choi
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
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In Search of a Universal Method: A Comparative Survey of Bottom-Up Proteomics Sample Preparation Methods
Increasing the power of interpretation for soil metaproteomics data
Increasing the throughput of sensitive proteomics by plexDIA
Individual species provide multifaceted contributions to the stability of ecosystems
iNEXT
Instrumentation at the Leading Edge of Proteomics
Interesting fact
IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs
iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
Jacek R. Wisniewski
Jana Seifert
Jean Armengaud
Jesper V. Olsen
Journals of interest
Juergen Cox
kernel estimation for CDF
key questions about SP3
KingFisher Flex System
KOLMOGOROV–SMIRNOV TEST
Krona
Laura Elo
LC configure
Lennart Martens
LFQRatio
Liang Qiao
Liang Tian
literature reading
Lloyd M Smith
loss of microbial cross feeding interactions
Lukas Käll
machine learning dataset
Machine learning VS deep learning
magnetic HILIC beads
Manuel Kleiner
Markup Reference
Marsilea: Declarative creation of composable visualization
Martin Wühr
Mass spectrometrists should only search for peptides they care about
Mass spectrometrists should search for all peptides, but assess only the ones they care about
MBR: match between run
MDA
Measuring turbidity
Meta4P
metacoder
MetaCoder
MetaNovo
Metaproteomic portrait of the healthy human gut microbiota
Metaproteomics and DNA metabarcoding as tools to assess dietary intake in humans
Metaproteomics Initiative
Metaproteomics to understand how microbiota function: The crystal ball predicts a promising future
Michael J. MacCoss
MiCId: Microorganism Classification and Identification
microbiome composition difference
microbiome relationship
Milestones of Metaproteomics
miniPhos in 2023
Mirror: An LLM-powered programming-by-example programming language
Modeling Lower-Order Statistics to Enable Decoy-Free FDR Estimation in Proteomics
MS QC tools
MS-DIAL
MS2Bac
MS²Rescore
mTRAQ
Mycoplasma
mzmine3
nanoLC design
network of big names
NeuCode Labels for Relative Protein Quantification
Nikolai Slavov
Non-mechanical disruption of Bacillus subtilis spores allows sensitive and deep characterization of the minimal proteome for resuming a cellular lifestyle
Nonlinear fitting method for determining local false discovery rates from decoy database searches
Not All About Proteomcs
Notes for Vanquish Neo HPLC
Oliver Fiehn
On the potential of micro-flow LC-MS/MS in proteomics
Only metaproteomics can inspect biomass based quantificiation
optimization of SP3 by the original author
Optimized Automated Workflow for BioID
Orbitrap Astral for Metabolomics
orochem.com
p value correction for multiple testing
PAcIFIC
Parallelized Acquisition of Orbitrap and Astral Analyzers Enables High-Throughput Quantitative Analysis
Pavel A Pevzner
PCA在R以及PCA 的数学意义解读
PCoA VS PCA
PECAN
PEP
PepGM
PepQuery
PepQuery2
peptide detectability: standard and effective
PeptideMapper
Peptonizer2000
Percolator
Perspective
Perspective and Guidelines for Metaproteomics in Microbiome Studies
Phosphopeptide enrichment Review
phyloseq
Picked Protein FDR
plagiarism figure by figure
Posterior error probabilities and false discovery rates: two sides of the same coin
Pratik Jagtap
predicted peptide detectability
Prediction of peptide mass spectral libraries with machine learning
Probability 概率
Prodigal
Protein Aggregation Capture on Microparticles Enables Multipurpose Proteomics Sample Preparation
Protein Contaminants Matter
protein digestion
ProteoBench
ProteoClade
Proteome depth reached in single-cell experiments
Proteomic stable isotope probing
Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation
prozor
PTXQC
q value
quantile normalization
QuantUMS
Qwen2
Qwen2.5-Coder
Rarefaction
razor peptide
reflection on Astral
report
resilience vs resistance
Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics
roadmap: learning resource
Robust and Easy-to-Use One-Pot Workflow for Label-Free Single-Cell Proteomics
Robust Capillary- and Micro-Flow Liquid Chromatography–Tandem Mass Spectrometry Methods for High-Throughput Proteome Profiling
Robust Microflow LC-MS/MS for Proteome Analysis: 38 000 Runs and Counting
Robust, Precise, and Deep Proteome Profiling Using a Small Mass Range and Narrow Window Data-Independent-Acquisition Scheme
Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC–MS/MS
Russians in proteins
Sage
Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics Based on Acid Extraction
sample preservation
scanning quadrupole
SCX for SDS cleanup
sequence of gluten peptide that are resistant to digestion
shared peptide problem for protein inference
SIMSI-Transfer: Software-Assisted Reduction of Missing Values in Phosphoproteomic and Proteomic Isobaric Labeling Data Using Tandem Mass Spectrum Clustering
Single-pot, solid-phase-enhanced sample preparation for proteomics experiments
SP3/PAC protocol
species redundancy
Species–function relationships shape ecological properties of the human gut microbiome
Spectra library search
Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins
SPEED, nanodiamond
Strategies for Increasing the Depth and Throughput of Protein Analysis by plexDIA
streptavidin-coupled bead
super pathway
Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics
Systematic Evaluation of Protein Reduction and Alkylation Reveals Massive Unspecific Side Effects by Iodine-containing Reagents
systmatic optimization of Phosphopeptide Enrichment for minute sample
TableOfContents
Techniques for clinical metaproteomics
The diversity–stability debate
The effect of peptide adsorption on signal linearity and a simple approach to improve reliability of quantification
The guild as a concept and a means in ecological parasitology
The Guild Concept and the Structure of Ecological Communities
The One Hour Human Proteome
The Simplified Human Intestinal Microbiota (SIHUMIx)
Thilo Muth
Ti4+-IMAC
Tiannan Guo
tiddlywiki grammar
Tim Van Den Bossche
Time to Result
timeline for misc
TMT cluster
TMT for quantitative proteomics
TMTpro reagent
to read
ToDo list
training resource
trap-and-elute
tree of life
Trypsin activity
Trypsin autolysis
two-step database search strategy
Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition
Unbiased Antimicrobial Resistance Detection from Clinical Bacterial Isolates Using Proteomics
Unified Human Gut Virome Catalog (UHGV)
Unified Workflow for the Rapid and In-Depth Characterization of Bacterial Proteomes
uniprot: peptide index and query
unique peptide VS distinct peptide
Updates of the In-Gel Digestion Method for Protein Analysis by Mass Spectrometry
Upper Limit of SDS for Tryptic Digestion
variable conditions of MS analysis
Virtual multi-Omics lab
VOGDB—Database of Virus Orthologous Groups
Weighted Kolmogorov Smirnov testing: an alternative for Gene Set Enrichment Analysis
what bacteria housekeeping proteins can be used for normalization in metaproteimcs
What database should mass spectrometrists search?
What fungi live in the gut? Meet the gut mycobiome
What is the total number of protein molecules per cell volume?
WikiMap
William Stafford Noble
Yang-yu Liu
Yangyang Bian
µPhos in 2024
为什么 VS Code 会这么牛逼？
先验概率与后验概率
参数方法与非参数方法
吲哚
基于深度学习的搜索引擎
大语言模型的速度为什么需要越来越快？
如何鉴定新的AMR基因或protein
常用 AI
序列比对
序列比对工具
接地气的
数据降维
核密度估计
格雷码
深度学习的框架哪家强？
王木头人工智能笔记
神经科学到深度学习
累积分布函数 cdf
线性代数与解析几何
细胞自动机
血清素
贝叶斯定量
逼近法
雌激素
音色