UC Davis Proteomics Online 2d Short Course

Created by Brett Phinney•22 Items•Updated October 01, 2020

Some videos we made to keep you occupied and to give you an idea of what our real proteomics 3d short courses are like. We will gradually add more and replace some of the audio when we get a better microphone. Sorry for the audio quality! For questions, updates and powerpoints register at ou… Show More

1

Go to Intro to Proteomics Brett Phinney with duration: 56 minutes, 8 seconds

Intro to Proteomics Brett Phinney

Created by Brett Phinney

Intro to Proteomics

proteomicsproteinspeptideslotproteinmassthingspeptidespectrometerkindlevelcouplespectrometerstimessampleacquisitionthousandsclassvideosmixture

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2

Go to Peptide Spectrum Matching using Data Dependent Acquisition (DDA) with duration: 1 hour, 4 minutes

Peptide Spectrum Matching using Data Dependent Acquisition (DDA)

Created by Brett Phinney

How we identify Peptides & Proteins from Tandem Mass Spectra using Data Dependant Acquisition

proteomicsmasspeptidespeptideproteinlotionsscoreproteinssequencethingsppmspectrometerspectratrypsindecoysspectrumterminusdatabaseenginesspectrometers

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3

Go to Data Independent Acquisition with duration: 1 hour, 8 minutes

Data Independent Acquisition

Created by Brett Phinney

Data Independent Acquisition overview

librarypeptidechromatogrampeptidesmasslotionslibrarieswindowsspectraproseintensityproteinsretentionpapersamplesminutestimesdaltonspectrometer

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4

Go to LCMS for Proteomics- part1 with duration: 59 minutes, 9 seconds

LCMS for Proteomics- part1

Created by Gabriela Grigorean

masspeptidepeptidesionfragmentationspectrometerspectrumionsphaseproteomicsanalytechargeinstrumentbeammsaminosamplemoleculespectrometryhplc

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5

Go to LCMS for Proteomics -part2 with duration: 26 minutes, 31 seconds

LCMS for Proteomics -part2

Created by Gabriela Grigorean

ionionsmotionmassvoltagetrapquadrupoledetectorrodselectronsanalyzerorbitrapsignalfieldcorkscrewshapefrequencyanalyzerselectrodeflightdimensionfragmentscircularimagerodthousandthdianequad

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6

Go to LCMS instrumentation lab Demo-part1 with duration: 22 minutes, 34 seconds

LCMS instrumentation lab Demo-part1

Created by Gabriela Grigorean

columnnanosampleneedlemasspreflowspectrometervalvebuffersamplermodulelooppumploadingpeptideslcmsliquidanalyzerspray

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7

Go to LCMS instrumentation lab Demo-part2 with duration: 30 minutes, 21 seconds

LCMS instrumentation lab Demo-part2

Created by Gabriela Grigorean

columnnanopeptidesmasspreresolutionacquisitionsamplemethodionpositionminutestrapbufferpeptideinjectionionsspectrometerpumploading

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8

Go to Guest Lecture. Ben Neeley NIST with duration: 50 minutes, 25 seconds

Guest Lecture. Ben Neeley NIST

Created by Brett Phinney

Our Guest Proteomics Expert for the course. Ben Neeley from NIST

bloodthingsproteinsmammalslothumanssamplesspecieslibrarygenomekindproteinbatsserummaterialsseaanalysistreegenomesproteomics

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9

Go to Sample Homogenization Using the Roche MagNA Lyser with duration: 8 minutes, 59 seconds

Sample Homogenization Using the Roche MagNA Lyser

Created by Justin Hocke

samplessampleproteinliverureaenzymerotorsdsprotocolcellsproteinstubesinhibitorsamountminutesretainermagnetdigestweisercycles

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10

Go to Protein Precipitation with duration: 8 minutes, 7 seconds

Protein Precipitation

Created by Michelle Salemi

precipitationproteinspelletliquidwashkitlossproteincentrifugesolutionbitbiochemacetoneethanolliverwasteminutesmicroliterscowmethod

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11

Go to Urea In Solution Digestion Wet Lab with duration: 55 minutes, 42 seconds

Urea In Solution Digestion Wet Lab

Created by Michelle Salemi

trypsinureasampledigestionmicrolitersspinproteinthingtfanitrileseedcolumnminutesbicarbonatesamplestubesstufflysinebitsolution

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12

Go to S-Trap Wet Lab Demonstration with duration: 7 minutes, 18 seconds

S-Trap Wet Lab Demonstration

Created by Brett Phinney

bufferdigestfiltersampleacidproteinbubblesairadditionsdstrapelutionvolumesolutionbondswash3dmicrogramssamplesspin

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13

Go to LCMS file visualisation with Qual Browser with duration: 12 minutes, 53 seconds

LCMS file visualisation with Qual Browser

Created by Gabriela Grigorean

peptidemstracemsmsfragmentationchromatogrammassintensitypeptidesscanspectrumrangeionpeakspeakwindowshapethinginstantmethod

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14

Go to Playing with raw dda data with duration: 18 minutes, 0 seconds

Playing with raw dda data

Created by Brett Phinney

looking at fusion lumos raw data

chromatogramionbasepeptidelotspectraorbitrappeakminutesbottomfreestylemsmsmsfilespeptidesbrowsermethodsmethodthermostuff

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15

Go to dia using dia-nn tutorial in real time. Yikes!! with duration: 1 hour, 13 minutes

dia using dia-nn tutorial in real time. Yikes!!

Created by Brett Phinney

real data analysis haha

libraryfilesretentionproteinskylinepeptideminutesrunpeakoutputpeptideslotguysthingskindsettingsdiasignalthingprose

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16

Go to dia-nn Part 2 with duration: 17 minutes, 42 seconds

dia-nn Part 2

Created by Brett Phinney

DIA using dia-nn part 2! We look at that really noisy peptide from last time and finally get it to look decent in Skyline!

proteomcis dialibraryskylinediapeptideprecursormobilityirtionproteinsstuffionssettingstransitionfragmentminuteminutesyesterdayalrightmspeaks

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17

Go to dia-nn part 3. Finishing up dia-nn and visualizing it in skyline with duration: 54 minutes, 19 seconds

dia-nn part 3. Finishing up dia-nn and visualizing it in skyline

Created by Brett Phinney

Here we finish up our dia-nn analysis and try to use skyline to visualize our peaks. Did it work? Humm...Maybe? You'll have to be the judge :)
Data can be found here

proteomicsmobilityionskylinelibrarypeptideminuteslotretentiondifferencepeptidespeaksprecursorirtthingspeaktransitionfilestimesimportsignal

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18

Go to MsFragger/FragPipe - a database search tool with duration: 42 minutes, 43 seconds

MsFragger/FragPipe - a database search tool

Created by Gabriela Grigorean

folderproteinexperimentmsproteinsfilesorganismswaggerpeptidemodificationkindphilosophercomputerrunbitdownloadintensityvaluesanalysisstuffdownloadsjarthingmodificationsppmhela

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19

Go to Using MSFragger and Skyline for diaPASEF experiments with duration: 58 minutes, 42 seconds

Using MSFragger and Skyline for diaPASEF experiments

Created by Brett Phinney

Using a ddaPASEF run we make a library using MSfragger and then use that in skyline for looking at diaPASEF experiments. Worked surprising well :)

proteomicsproteinslibrarypeptideslotdecoyspeakrunskylinemodelthingspeptideforagerretentionmobilityfilesdotminuteminutesproblemms

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20

Go to De Novo Take 1 with duration: 25 minutes, 39 seconds

De Novo Take 1

Created by Michelle Salemi

practice kind of think I dropped an F bomb

ionspeptidemassspectrumb2aminoacidthinglysinesideendionargininemsmsacidsfragmentationlossammoniumwaterpair

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21

Go to De Novo Computer and paper problems with duration: 32 minutes, 45 seconds

De Novo Computer and paper problems

Created by Michelle Salemi

masspeptideaminothingmassesleucinethingsmsmsb2acidsworksheetsequenceansweracidbitpeakionsamuminusisoleucine

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22

Go to Pulling and Packing Nanocolumns with duration: 47 minutes, 14 seconds

Pulling and Packing Nanocolumns

Created by Brett Phinney

columnnanosilicatiplasermillisecondstipscolumnskindpointheatingguysslurryparticlespullglassreasonenergyvelocitygold

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