Biomarker Search

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this was the original slide

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data from

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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

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[acesnik]

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.