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topdownproteomics / sdk

Software solution for common top-down proteomics tasks
http://www.topdownproteomics.org/
MIT License
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Biomarker Search #34

Open trishorts opened 6 years ago

trishorts commented 6 years ago

this was the original slide image

trishorts commented 6 years ago

data from image

trishorts commented 6 years ago

Here are a couple lines from the excel file. I guess there is the complete aa sequence so no worries. but ther are massive "unlocalized" mass shifts. I think these can be dealt with using the unlocalized mass shift results we discussed. so maybe not an actual issue. Here is some of the table.

Protein Description Sequence Theoretical Mass Observed Mass Mass Difference (Da) Mass Difference (ppm) Fragmentation type Search type Matching fragments P-Score q-value
>SC6B2_YEAST, P52871, RecName: Full=Protein transport protein SEB2; AltName: Full=Ssh1 complex subunit SEB2; AltName: Full=Ssh1 complex subunit beta;. (Acetylation)AASVPPGGQRILQKRRQAQSIKEKQAKQTPTSTRQAGYGGSSSSILKLYTDEANGFRVDSLVVLFLSVGFIFSVIALHLLTKFTHII 9511.21 9397.132777 -114.072 -12139.1 CID absolute mass 13 9.20E-13 4.36E-08
>HSP75_YEAST, P11484, RecName: Full=Heat shock protein SSB1; AltName: Full=Cold-inducible protein YG101;. (Acetylation)AEGVFQGAIGIDLGTTYSCVATYESSVEIIANEQGNRVTPSFVAFTPEERLIGDAAKNQAALNPRNTVFDAKRLIGRRFDDESVQKDMKTWPFKVIDVDGNPVIEVQYLEETKTFSPQEISAMVLTKMKEIAEAKIGKKVEKAVITVPAYFNDAQRQATKDAGAISGLNVLRIINEPTAAAIAYGLGAGKSEKERHVLIFDLGGGTFDVSLLHIAGGVYTVKSTSGNTHLGGQDFDTNLLEHFKAEFKKKTGLDISDDARALRRLRTAAERAKRTLSSVTQTTVEVDSLFDGEDFESSLTRARFEDLNAALFKSTLEPVEQVLKDAKISKSQIDEVVLVGGSTRIPKVQKLLSDFFDGKQLEKSINPDEAVAYGAAVQGAILTGQSTSDETKDLLLLDVAPLSLGVGMQGDMFGIVVPRNTTVPTIKRRTFTTCADNQTTVQFPVYQGERVNCKENTLLGEFDLKNIPMMPAGEPVLEAIFEVDANGILKVTAVEKSTGKSSNITISNAVGRLSSEEIEKMVNQAEEFKAADEAFAKKHEARQRLESYVASIEQTVTDPVLSSKLKRGSKSKIEAALSDALAALQIEDPSADELRKAEVGLKRVVTKAMSSR 66471.5 11093.86397 -55377.7 -4991740 CID absolute mass 11 6.44E-10 3.79E-05
>VATF_YEAST, P39111, RecName: Full=V-type proton ATPase subunit F; Short=V-ATPase subunit F; AltName: Full=V-ATPase 14 kDa subunit; AltName: Full=Vacuolar proton pump subunit F;. (Acetylation)AEKRTLIAVIADEDTTTGLLLAGIGQITPETQEKNFFVYQEGKTTKEEITDKFNHFTEERDDIAILLINQHIAENIRARVDSFTNAFPAILEIPSKDHPYDPEKDSVLKRVRKLFGE 13363.9 13372.94921 9.00642 673.48 CID absolute mass 30 3.65E-38 5.67E-39
>CYB_YEAST, P00163, RecName: Full=Cytochrome b; AltName: Full=Complex III subunit 3; AltName: Full=Complex III subunit CYTB; AltName: Full=Complex III subunit III; AltName: Full=Cytochrome b-c1 complex subunit 3; AltName: Full=Cytochrome b-c1 complex subunit CYTB; AltName: Full=Ubiquinol-cytochrome-c reductase complex cytochrome b subunit;. (Acetylation)AFRKSNVYLSLVNSYIIDSPQPSSINYWWNMGSLLGLCLVIQIVTGIFMAMHYSSNIELAFSSVEHIMRDVHNGYILRYLHANGASFFFMVMFMHMAKGLYYGSYRSPRVTLWNVGVIIFILTIATAFLGYCCVYGQMSHWGATVITNLFSAIPFVGNDIVSWLWGGFSVSNPTIQRFFALHYLVPFIIAAMVIMHLMALHIHGSSNPLGITGNLDRIPMHSYFIFKDLVTVFLFMLILALFVFYSPNTLGHPDNYIPGNPLVTPASIVPEWYLLPFYAILRSIPDKLLGVITMFAAILVLLVLPFTDRSVVRGNTFKVLSKFFFFIFVFNFVLLGQIGACHVEVPYVLMGQIATFIYFAYFLIIVPVISTIENVLFYIGRVNK 43537.8 938.814778 -42598.9 -45375200 SID absolute mass 4 8.33E-09 4.46E-04
>CPD1_YEAST, P53314, RecName: Full=2',3'-cyclic-nucleotide 3'-phosphodiesterase; Short=CPDase; EC=3.1.4.37;. (Acetylation)AIALWYCPPQGSVAYETLQMLIFSFQTLFPDSPVFEPHVTVTSHLVCNSKDDVNKILTSCVAAIQSIRSHQTAKKGRKGQVSHAVAAPLVSFNGCSVGKQYFKKIVLECNKNKILYGVAQVMREMYVEIDPETRSSRAATWVHEEFHPHVSLLYSDIHPVSQASLRVVQQRIEDALDVQLVPREKRKGSGNADGSNEVQMRWDFDVSSSLSWNIPGTFKVVNCVGPVQEWEVLGRVDV 26625.5 10452.46359 -16173 -1547300 SID absolute mass 4 1.11E-06 3.05E-02
>NCB5R_YEAS7, A6ZVM6, RecName: Full=NADH-cytochrome b5 reductase 1; EC=1.6.2.2; AltName: Full=Microsomal cytochrome b reductase; AltName: Full=P35;. (Acetylation)AIDAQKLVVVIVIVVVPLLFKFIIGPKTKPVLDPKRNDFQSFPLVEKTILTHNTSMYKFGLPHADDVLGLPIGQHIVIKANINGKDITRSYTPTSLDGDTKGNFELLVKSYPTGNVSKMIGELKIGDSIQIKGPRGNYHYERNCRSHLGMIAGGTGIAPMYQIMKAIAMDSHDTTKVSLVFGNVHEEDILLKKELEALVAMKPSQFKIVYYLDSPDREDWAGGVGYITKDVIKEHLPAATVDNVQILICGPPAMVASVRRSTVDLGFRRSKPLSKMEDQVFVF 31312.6 6433.486184 -24879.1 -3867120 SID absolute mass 5 1.56E-06 3.95E-02
>RL26A_YEAST, P05743, RecName: Full=60S ribosomal protein L26-A; AltName: Full=L33; AltName: Full=YL33;. (Acetylation)AKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIRRDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHPSKLVITKLHLDKDRKALIQRKGGKLE 14136 9036.197066 -5099.84 -564380 CID absolute mass 17 2.88E-22 4.99E-19
>PKR1_YEAST, Q03880, RecName: Full=V-type ATPase assembly factor PKR1;. (Acetylation)ANFFVRLWESVFEPGTSPQLIIATHVSFVALLLTLIWLIYATNGNIHFYALFCISLLLWITVIWFINELSHVKLKDNDELDKDANKKDDSAIKEDSEDKQESGKSTSTARRTQAQSRSRKA 13864.2 19473.23813 5609.01 288037 SID absolute mass 16 2.53E-22 4.26E-19
>HSP31_YEAST, Q04432, RecName: Full=Probable chaperone protein HSP31; EC=3.2.-.-; AltName: Full=Heat shock protein 31;. (Acetylation)APKKVLLALTSYNDVFYSDGAKTGVFVVEALHPFNTFRKEGFEVDFVSETGKFGWDEHSLAKDFLNGQDETDFKNKDSDFNKTLAKIKTPKEVNADDYQIFFASAGHGTLFDYPKAKDLQDIASEIYANGGVVAAVCHGPAIFDGLTDKKTGRPLIEGKSITGFTDVGETILGVDSILKAKNLATVEDVAKKYGAKYLAPVGPWDDYSITDGRLVTGVNPASAHSTAVRSIDALKN 25565 25568.00369 3.00914 117.692 SID absolute mass 10 2.62E-15 6.82E-11
>TKT2_YEAST, P33315, RecName: Full=Transketolase 2; Short=TK 2; EC=2.2.1.1;. (Acetylation)AQFSDIDKLAVSTLRLLSVDQVESAQSGHPGAPLGLAPVAHVIFKQLRCNPNNEHWINRDRFVLSNGHSCALLYSMLHLLGYDYSIEDLRQFRQVNSRTPGHPEFHSAGVEITSGPLGQGISNAVGMAIAQANFAATYNEDGFPISDSYTFAIVGDGCLQEGVSSETSSLAGHLQLGNLITFYDSNSISIDGKTSYSFDEDVLKRYEAYGWEVMEVDKGDDDMESISSALEKAKLSKDKPTIIKVTTTIGFGSLQQGTAGVHGSALKADDVKQLKKRWGFDPNKSFVVPQEVYDYYKKTVVEPGQKLNEEWDRMFEEYKTKFPEKGKELQRRLNGELPEGWEKHLPKFTPDDDALATRKTSQQVLTNMVQVLPELIGGSADLTPSNLTRWEGAVDFQPPITQLGNYAGRYIRYGVREHGMGAIMNGISAFGANYKPYGGTFLNFVSYAAGAVRLAALSGNPVIWVATHDSIGLGEDGPTHQPIETLAHLRAIPNMHVWRPADGNETSAAYYSAIKSGRTPSVVALSRQNLPQLEHSSFEKALKGGYVIHDVENPDIILVSTGSEVSISIDAAKKLYDTKKIKARVVSLPDFYTFDRQSEEYRFSVLPDGVPIMSFEVLATSSWGKYAHQSFGLDEFGRSGKGPEIYKLFDFTADGVASRAEKTINYYKGKQLLSPMGRAF 74893.7 15708.53435 -59185.1 -3767710 SID absolute mass 6 1.31E-11 7.23E-07
>AAD15_YEAST, Q08361, RecName: Full=Putative aryl-alcohol dehydrogenase AAD15; EC=1.1.1.-;. (Acetylation)ARHFGMALAPWDVMGGGRFQSKKAMEERRKNGECIRSFVGASEQTDAEIKISEALAKVAEEHGTESVTAIAIAYVRSKAKNVFPSVEGGKIEDLKENIKALSIDLTPDNIKYLENVVPFDIGFPNTFIVLNSLTQKYGTNNV 15623 15695.02762 71.9951 4587.13 SID absolute mass 3 1.45E-06 3.73E-02
>TPIS_YEAST, P00942, RecName: Full=Triosephosphate isomerase; Short=TIM; EC=5.3.1.1; AltName: Full=Triose-phosphate isomerase;. (Acetylation)ARTFFVGGNFKLNGSKQSIKEIVERLNTASIPENVEVVICPPATYLDYSVSLVKKPQVTVGAQNAYLKASGAFTGENSVDQIKDVGAKWVILGHSERRSYFHEDDKFIADKTKFALGQGVGVILCIGETLEEKKAGKTLDVVERQLNAVLEEVKDWTNVVVAYEPVWAIGTGLAATPEDAQDIHASIRKFLASKLGDKAASELRILYGGSANGSNAVTFKDKADVDGFLVGGASLKPEFVDIINSRN 26689.9 26698.74389 8.81027 329.988 SID absolute mass 20 1.41E-30 2.77E-29
>EMP24_YEAST, P32803, RecName: Full=Endosomal protein P24B; AltName: Full=24 kDa endomembrane protein; AltName: Full=Basic 24 kDa late endocytic intermediate component; Flags: Precursor;. (Acetylation)ASFATKFVIACFLFFSASAHNVLLPAYGRRCFFEDLSKGDELSISFQFGDRNPQSSSQLTGDFIIYGPERHEVLKTVRDTSHGEITLSAPYKGHFQYCFLNENTGIETKDVTFNIHGVVYVDLDDPNTNTLDSAVRKLSKLTREVKDEQSYIVIRERTHRNTAESTNDRVKWWSIFQLGVVIANSLFQIYYLRRFFEVTSLV 23228.7 7787.469835 -15441.3 -1982840 SID absolute mass 3 1.11E-06 3.05E-02
>RL32_YEAST, P38061, RecName: Full=60S ribosomal protein L32;. (Acetylation)ASLPHPKIVKKHTKKFKRHHSDRYHRVAENWRKQKGIDSVVRRRFRGNISQPKIGYGSNKKTKFLSPSGHKTFLVANVKDLETLTMHTKTYAAEIAHNISAKNRVVILARAKALGIKVTNPKGRLALEA 14673.2 5357.830591 -9315.37 -1738650 CID absolute mass 7 1.28E-08 6.68E-04
trishorts commented 6 years ago

screen shot looks like --> image

acesnik commented 6 years ago

Was the point here to consider annotating large unlocalized "modifications" using ProForma? Or perhaps to start the discussion about what to do with these giant mass shifts that we see in TopDownPortal results when considering writing them in ProForma? I can't quite remember.