The rockefeller university

Some useful information, protocols and software can be found at the following web pages.

• ProteomeDiscoverer (v1.4)/Mascot cheat sheet.
• StaGE tips. StaGE (stop-and-go extraction) tips are used for micro solid phase purification (SPE). They can be purchased or made easily in the laboratory. A wide variety of 3M Empore membranes (SAX, SCX, C₈ etc.) are available.  See how to make a StaGE tip in this video.
  Orginal publication on StaGE tips by Yasushi Ishihama can be found following this link: http://www.ncbi.nlm.nih.gov/pubmed/12585499 & http://www.ncbi.nlm.nih.gov/pubmed/16602707
• MS search tools from the Brian Chait lab: http://www.rockefeller.edu/labheads/chait/tools.php
• Proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments: http://prospector.ucsf.edu/
• Calculation of fragment ions: https://prospector.ucsf.edu/prospector/cgi-bin/msform.cgi?form=msproduct
• Link to off campus (limited) MASCOT tandem MS searchserver: http://www.matrixscience.com/search_form_select.html
• Protocols from the Mike Rout lab: http://lab.rockefeller.edu/rout/protocols
• Link to structural description of some common detergents: http://www.proteinsandproteomics.org/content/free/tables_1/table14.pdf
• From cells to proteins sequence from the Steen lab at Childrens Hospital: http://www.childrenshospital.org/research/_proteomics/index.html
• An introduction to tandem MS data analysis using search algorithms: http://www.proteomesoftware.com/MS_MS_Results.html
• Wikipedia overview of some Mass spectrometry softwares: http://en.wikipedia.org/wiki/Mass_spectrometry_software
• List of lipids and related tools: http://www.lipidmaps.org/
• Create sequence logo: http://weblogo.berkeley.edu/logo.cgi
• To create sequence logo/find motifs (prefered tool): http://iomics.ugent.be/icelogoserver/main.html
• Software: http://omics.pnl.gov/software/software_alphabetical.php
• To send large files (For RU only) https://elf.rockefeller.edu//
• NIST Libraries of Peptide Tandem Mass Spectra: http://peptide.nist.gov/
• Peptide and Protein Identification Tutorial (by Harald Barsnes  Marc Vaudel): http://compomics.com/peptide_and_protein_identification_tutorial/
• Denovo: http://proteomics.ucsd.edu/LiveSearch/
• MALDI sample preparation (The Ultra Thin Layer Method): http://prowl.rockefeller.edu/protocols/ultra-thin-layer.html
• UniProt (Complete Proteomes – exampel shown for S Pombe): http://www.uniprot.org/uniprot/?query=organism%3A%22Homo+sapiens+%5b9606%5d%22+AND+keyword%3A%22Complete+proteome+%5bKW-0181%5d%22&sort=score
• Selected MaxQuant summer school videos from the MaxQuant youtube channel: http://www.youtube.com/channel/UCKYzYTm1cnmc0CFAMhxDO8w.
• Mass spectrometry based proteomics tutorials from the Lamond Lab:
  http://www.lamondlab.com/MSResource/index.php
• To download a demo version of ProteomeDiscoverer from Thermo, click here, and register. The demo version is fully active for 30 days whereafter it will become a viewer-only which can open .msf files, the data format of ProteomeDiscoverer.
• Denovo sequencing: Graphic user interface for PepNovo+: https://code.google.com/p/denovogui/
• CPU benchmarking: http://www.cpubenchmark.net/
• Crosslink antibody to Dynabeads: http://www.lifetechnologies.com/us/en/home/references/protocols/proteins-expression-isolation-and-analysis/immunoprecipitation-protocol/immunoprecipitation-crosslinking.html
• Find Chemical Structures: http://www.tcichemicals.com/eshop/en/us/catalog/list/structure/
• CRAPome – test your list of matched proteins aginst more than 400 co-IP’s: http://www.crapome.org/?q=wk_1_1_search
• Calculation and graphic presentations of Isotopic Patterns: http://www.envipat.eawag.ch/index.php
• The End of ‘Genius’ by J. W. Shenk (maybe a comment re. co-authorships): http://nyti.ms/1rqZlqX
• The Contaminant Repository for Affinity Purification (CRAPome): http://www.crapome.org/
• Denovo tables: http://www.ionsource.com/tutorial/DeNovo/denovo_tables.htm
• Flip text: http://textmechanic.com/Reverse-Text-Generator.html
• Prediction of Transmembrane helices in proteins (TMHMM 2.0): http://www.cbs.dtu.dk/services/TMHMM/
• Generate VENN diagrams: http://bioinfogp.cnb.csic.es/tools/venny/
• Statistical calc. and Microsoft Excel (Video tutorials): http://ehealth.kcl.ac.uk/sites/physiology/?videoscategory=ms-office
• P– vs Q– vs PEP-values in Mass Spec Database Search: https://bioinfomagician.wordpress.com/2013/10/14/p-vs-q-vs-pep-values-in-mass-spec-database-search/
• Metabolomic pathway analysis: http://pathways.embl.de/ (http://pathways.embl.de/iPath2.cgi#)
• Protein Structures at a glance (http://www.ncbi.nlm.nih.gov/pubmed/25633501): http://aquaria.ws/
• Elution of biotin from streptavidin: http://www.lifetechnologies.com/us/en/home/brands/product-brand/dynal/streptavidin-coupled-dynabeads/elution-of-the-streptavidin.html
• CMPD (Cancer Mutant Proteome Database). In addition to full protein sequences, shorter sequences that can accommodate a few missed tryptic cleavages are available: http://120.126.1.62/cmpd/
• ProteomicsDB: https://www.proteomicsdb.org/
• STRING – Known and Predicted Protein-Protein Interactions: http://string-db.org/
• Immobilization of antibody tricks: http://www.lifetechnologies.com/us/en/home/life-science/protein-biology/protein-assays-analysis/immunoprecipitation/immunoprecipitation-dynabeads-other-magnetic-beads.html
• Useful bio numbers: http://kirschner.med.harvard.edu/files/bionumbers/fundamentalBioNumbersHandout.pdf
• Regular expression test page: https://regex101.com/
• A Biologist’s Field Guide to Multiplexed Quantitative Proteomics.
• The online journal club: https://pubpeer.com/
• http://biocyc.org/
• http://proteomicsnews.blogspot.com/
• MS-STATS http://msstats.org/
• Video about proteomics research from the Heck Lab: https://youtu.be/1G6jTGAfgUc…useful to promote proteomics research worldwide and to be used for education and teaching.
• Phospho network analysis
• BCA (protein conc. measurements from Pierce) compatibility table BCA:
• NanoSight in 90 seconds: https://www.youtube.com/watch?v=DMdvmHI4wsg
• Accurate mass to atomic composition and vice versa: http://www.chemcalc.org/mf_finder/mfFinder_em_new
• FUNRICH (FunRich: Functional Enrichment analysis tool)
• REACTOME
• Jens’ List common keratin and trypsin peptides and their of fragment ions (HCD).
• Peptide Extractor (PepEX). Requires Python Anaconda
• Peptidoglycan details. Source: http://onlinelibrary.wiley.com/doi/10.1002/9780470015902.a0021974/pdf
• MASSive – MS data sharing http://massive.ucsd.edu/ProteoSAFe/static/massive.jsp
• http://www.mycompoundid.org/mycompoundid_IsoMS/
• https://xcmsonline.scripps.edu/landing_page.php?pgcontent=mainPage
• GCMS notes: http://www.scientific.org/tutorials/articles/gcms.html
• Albert Heck’s web site: https://www.hecklab.com/
• Kuster’s Human Proteome DB: www.proteomicsdb.org/
• Merge files: https://www.computerhope.com/issues/ch001376.htm
• Perseus & PTMs. Excellent step-by-step instruction (http://www.coxdocs.org/doku.php?id=perseus:user:use_cases:modifications). Another good tutorial for data analysis in Perseus: http://www.zmbh.uni-heidelberg.de/Central_Services/Mass_Spectrometry/PDF/150206%20Perseus%201.5.1.5%20Tutorial_Version2.pdf
• PhosphoSitePlus
• Rune Matthiesien’s Introduction to Mass Spectrometry-Based Proteomics
• Isotope Calculator: https://www.envipat.eawag.ch/index.php
• Complete De Novo Assembly of Monoclonal Antibody Sequences. The ALPS software (de Bruijn assembly software – command line) is available at: https://static-content.springer.com/esm/art%3A10.1038%2Fsrep31730/MediaObjects/41598_2016_BFsrep31730_MOESM2_ESM.zip
• HLA1 peptide prediction tool: http://www.cbs.dtu.dk/services/NetMHCpan/
• Convert UniProt accessions numbers to GENE NAMES: https://www.uniprot.org/uploadlists/
• Mass bank of North America
• PRC Resource Center Presentation (April 21 2021) https://rocku.zoom.us/rec/share/ZnAIQDA13ZzaSp5YJ-qhVST4y3nHcUH73dEQ5gR44fHq2J4-TX1zZzLc659QyH-W.cNgQ9S2A-k0ZXkkC . Access Passcode: PDP5H?.e
• Recycle of plastics (as of Summer 2022).
• Protein Abundance Database: https://pax-db.org/
• Conversion of metabolites names into KEGG or HMDB: https://www.metaboanalyst.ca/MetaboAnalyst/upload/ConvertView.xhtml
• P-values, False Discovery Rate (FDR) and q-values: https://www.nonlinear.com/support/progenesis/comet/faq/v2.0/pq-values.aspx
• Glycosylation, oxonium fragment ions (table 1) : https://pubs.acs.org/doi/epdf/10.1021/pr0700605?ref=article_openPDF
• Plasma depletion by acid precipitation by Hanno: https://pubmed.ncbi.nlm.nih.gov/36989362/
• Review/test of plasma depletion strategies by Coon (Technical Evaluation of Plasma Proteomics Technologies from 2025)
• Another Plasma enrichment/depletion comparison: https://www.biorxiv.org/content/10.1101/2025.11.03.686186v1